APR

Wheat leaf rust (LR) and stripe rust (YR), caused by the air-borne fungi Puccinia triticina (Pt) and Puccinia striiformis f. sp. tritici (Pst), respectively, are considered the primary biotic threats to bread wheat and durum wheat production globally. Growing resistant wheat varieties is a key method of minimizing the extent of yield losses caused by these diseases. Bread wheat lines Francolin #1, Kenya Kongoni, Kundan and Sujata, and CIMMYT-derived durum wheat lines Bairds and Dunkler display an adequate level of adult plant resistance (APR) to both leaf rust and stripe rust in Mexican field environments. Six recombinant inbred line (RIL) populations developed from crosses Avocet/Francolin #1, Avocet/Kenya Kongoni, Avocet/Kundan, Avocet/Sujata, Atred#1/Bairds and Atred#1/Dunkler were phenotyped for leaf rust response at Ciudad Obregon, Mexico, and the bread wheat populations for stripe rust response at Toluca for under artificial inoculations for multiple seasons. The RIL populations and their parents were genotyped with the 50 K diversity arrays technology (DArT) sequence system and simple sequence repeat (SSR) markers. Known pleotropic APR genes Lr46/Yr29 mapped in all of six populations, and explained 7.4-65.1% and 7.7-66.1% severity variations for LR and YR across different bread wheat populations and accounted for 12.4-60.8% of LR severity variations over two durum wheat populations. In addition, several new APR loci identified on chromosomes 1AS, 1DS, 2BS, 2BL, 3D and 7BL in bread wheat and QTL on chromosome 6BL in durum wheat. Among these loci, QTL on chromosomes 1AS, 3D and 7BL might be represent new co-located/pleotropic loci conferring APR to LR and YR. RILs combining these APR loci can be used as sources of complex APR in both bread wheat and durum wheat breeding. In addition, the closely linked single nucleotide polymorphism (SNP) markers have been converted into breeder-friendly kompetitive allele specific PCR (KASP) markers and their diagnostic verified.

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.     

Elite barley breeding lines from the Australian Northern Region Barley Breeding Program were evaluated at the seedling and adult growth stages for resistance to leaf rust (LR) caused by Puccinia hordei. F3:5 lines derived from parental germplasm of different geographic origins were screened in the glasshouse and field spanning four years of trials. The 2009 and 2011 breeding populations (BP1 and BP2) comprised 360 lines and were genotyped with 3,244 polymorphic diversity arrays technology (DArT) markers. The 2012 and 2013 breeding populations (BP3 and BP4) comprised 320 lines genotyped with the DArT GBS array (DArTseq), providing 15,400 high quality polymorphic markers. Association mapping (AM) using the DArT/DArT-seq datasets and phenotypic data from 15 independent LR response assays identified a number of genomic regions associated with resistance. The BP1 and BP2 study detected a total of 15 QTL; 5 QTL co-located with catalogued LR resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, and Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. Markers in common between the DArT and DArTseq datasets enabled integration of mapping results for LR response across the four breeding populations and all QTL detected were visualised on a single map for validation. The adult plant resistance (APR) locus Rph20 was the only region detected in all field environments. Markers and their associated sequences identified in this study will be useful for building QTL combinations involving Rph20, thereby providing stable LR resistance in improved barley cultivars. We will also highlight the advantages of AM using breeding germplasm over traditional bi-parental mapping approaches that underutilise genetic diversity and divert valuable resources into populations of low breeding value.

A set of 63 wheat landraces obtained from Institute of Agri-Biotechnology and Genetic Resources, NARC-Islamabad was screened for adult plant resistance (APR) at two inoculated locations during the 2012-13 cropping season, i.e. Wheat Research Institute (WRI), Faisalabad, for leaf rust and Cereal Crops Research Institute (CCRI), Pirsabak, for stripe rust. Responses based on coefficients of infection (CI) were recorded. Five landraces were susceptible (CI >60) and 39 were resistant to both rusts at the adult plant stage; 47 lines were resistant to leaf rust and 51 were resistant to stripe rust, with CI values of 0-20. Four landraces had moderate levels of APR (CI 21-40) to both rusts, 12 to leaf rust and 8 to stripe rust. Only two landraces (accessions 10975 and 11029) showed MR/MS reactions, and one (11438) had an MS/S reaction; the remaining produced S reactions to leaf rust at WRI. At CCRI Pirsabak, the majority of lines responded with MR/MRMS reactions, the remaining lines were susceptible. The 39 landraces identified to have resistance to both diseases may carry new APR gene(s) to one or both rusts, but must be further characterized prior to use as parents in national wheat breeding programs.