leaf rust

Leaf rust is endemic to all wheat-growing regions of the world. Resistance to leaf rust in wheat cultivars is controlled either by all stage resistance (ASR) or by adult plant resistance (APR) genes. Although deployment of single ASR genes can provide high levels of resistance, these are usually overcome by virulence in pathogen populations. In contrast, individual APR genes often provide low levels of resistance and combinations of three to four genes are necessary to achieve adequate resistance for crop protection. This kind of APR has proven to be durable. APR gene Lr48 in a single plant selection of Condor (CSP44) was mapped on chromosome 2BS and was flanked by markers gwm429b (6.1 cM, distal) and barc7 (7.3 cM, proximal) (Bansal et al. 2008, Theor. Appl. Genet. 117:307-312). The present study was planned to identify markers more closely linked to Lr48. Selective genotyping by 90K Infinium Assay identified 27 SNP markers linked with Lr48. The SNP sequences were used to design Kompetitive Allele-Specific Primers (KASP). Eleven KASP markers showing clear clustering were genotyped on a RIL population using the CFX96 Touch™ real-time PCR detection system (Biorad, USA). KASP marker IWB72894 co-segregated with Lr48.

The quest for durable rust resistance in wheat is burgeoning with the emergence of new virulent races. Breeders challenged with this unceasing plant-pathogen arms race have to devise strategies for effective evaluation and exploitation of the rust resistance genes. Considering the likely presence of useful variation for rust resistance in CIMMYT’s international bread wheat screening nurseries (IBWSN), we implemented genomic prediction in the 45^th and 46^th IBWSN entries to determine their genomic estimated breeding values (GEBV’s) for leaf, stem and stripe rust resistance. The 350 lines (45^th IBWSN) and 329 lines (46^th IBWSN) were phenotyped in replicated trials over two to three years in El Batan, Mexico (leaf rust); Njoro, Kenya (stem rust) and Toluca, Mexico (stripe rust). The filtered genotyping data for these two nurseries comprised of 6,786 and 11,218 genotyping by sequencing (GBS) markers. Our objective was to compare the GEBV’s estimated by four different models: multiple linear regression (MLR) with QTL-linked markers as fixed effects; Genomic-best linear unbiased prediction (G-BLUP); G-BLUP mixed model which includes QTL linked markers as fixed effects and Bayesian least absolute shrinkage and selection operator (LASSO). We observed that the prediction accuracies (calculated using 10-fold cross validation) were the highest for stripe rust (0.52 to 0.61), followed by stem rust (0.42 to 0.65) and leaf rust (0.15 to 0.45). Among the models, the MLR gave the lowest prediction accuracies (0.15,0.42 and 0.52), while G-BLUP (0.45,0.59 and 0.59), mixed G-BLUP (0.38,0.65 and 0.62) and the Bayesian LASSO (0.45,0.58 and 0.61) yielded relatively higher and almost similar accuracies. Overall, our results are promising and indicate that using genome-wide markers is advantageous than including only significant QTL-linked markers. We hope that implementing genomic prediction in breeding programs, would help to achieve rapid gains from selection and revolutionize our efforts in combating the rust pathogen.

Wheat is one of the three most important food crops of Nepal for which rusts (Puccinia triticina, P.striiformis and P.graminis) are major biotic stresses. Leaf rust is widespread and causes 14-20% yield losses and speculated that P.triticina over summer on self-sown wheat in hills of Nepal. Twenty two different pathotypes of P.triticina have been recorded while thirteen leaf rust resistant genes (Lr1, Lr3, Lr10, Lr13, Lr14a, Lr16, Lr17, Lr19, Lr23, Lr26, Lr27, Lr31 and Lr34) either singly or in combinations, impart resistance to wheat genotypes in Nepal. Yellow rust is also a major disease in mid and lower hills, river basin and valleys, causing 30-80 % grain yield losses. Twenty-nine pathotypes of P.striiformis have been recorded till now in Nepal while nine Yr genes (Yr2, Yr2 KSA, YrA, Yr6, Yr7, Yr9, Yr27, GA, and SU) have been postulated. Stem rust is a minor and sporadic disease in central, western, mid-western region late in the season. Nine Sr genes (Sr2, Sr5, Sr7b, Sr8, Sr8a, Sr9b, Sr11, Sr25 and Sr31) have been characterized. Vijay was the first Ug99 resistant wheat variety released for cultivation. Previous experiences show that Nepal served as a focal point of wheat rusts for further spread in the Gangetic plains of India due to presence of more than 25 species of Berberis in hills of Nepal. Efforts are underway to survey rusts infection on Berberis spp. Use of Tilt (Propiconazole), Triadimefon (Bayleton) and Indar (RH-124) was found effective to reduce leaf rust as well as foliar blight. Cultivation of resistant varieties in Nepal not only reduces rust severity in this country but also minimizes crop losses in other neighboring countries especially India. This demands the need for regional collaboration in South Asia to combat wheat rusts.

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.