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A key objective of BGRI is to breed high yielding, stem rust resistant spring wheat germplasm suitable for releases as successful varieties in wheat growing countries of Africa, Middle East, Asia and Latin America. High emphasis was given to select adult plant resistance (APR) to stem rust in achieving this goal that is especially important in East African highlands where various variants belonging to the Ug99 race group and other lineages of stem rust fungus are now known, disease is endemic and present throughout the year on wheat crops. Recent molecular mapping studies show that combinations of partially effective APR gene Sr2 with 3 to 4 additional APR genes such as Sr55, Sr56, Sr57, Sr58 and other undesignated quantitative trait loci confer adequate to high levels of resistance to stem rust. A ‘Mexico-Kenya shuttle breeding scheme’ was initiated in 2008 to select APR to stem rust under high disease pressures at Njoro, Kenya while selecting for resistance to other rusts, yield, agronomic and quality traits in Mexico. This selection scheme, combined with phenotyping of advanced lines for multiple seasons in Kenya has resulted in identifying a small frequency of high yielding lines that possess a high level of resistance with a stable and low stem rust severity performance over seasons/locations under high disease pressures. These near-immune wheat lines are the best candidates for release in East Africa to achieve durable disease control and simultaneously curtail, or reduce, further selection of new virulences. A significantly higher proportion of wheat lines were also developed with moderate levels of resistance that is considered suitable for deployment in wheat growing areas where rust builds up later in the season. The worldwide distribution of the wheat lines derived from Mexico-Kenya shuttle breeding initiated in 2012 through the international yield trials and nurseries from CIMMYT. Potential releases and cultivation of these lines in different countries together with a reduction in area sown to susceptible varieties are expected to reduce the threat from stem rust.
The stem rust resistance genes Sr31 and Sr50 in wheat were both derived from translocations of the short arm of chromosome 1 from rye and conferred resistance to all field isolates of Puccinia graminis f. sp tritici (Pgt) for many years, preventing their distinction as different resistance specificities. We now show that Sr50 confers resistance against the Ug99 strain that overcomes Sr31, whereas a mutant Pgt strain virulent towards Sr50 is avirulent towards Sr31. Because lack of recombination between wheat and rye chromosome arms precludes genetic mapping and so map-based cloning of Sr50, we used a combination deletion mutagenesis and large DNA fragment cloning in bacterial artificial chromosome (BAC) vectors to define this resistance locus. Sequence analysis of a BAC contig spanning the smallest deletion detected with DNA markers at the Sr50 locus identified six coiled coil nucleotide binding site leucine-rich repeat (CC-NB-LRR) genes and a chymotrypsin inhibitor gene closely related to genes at the orthologous barley powdery mildew resistance locus, Mla. Sequencing of these genes from two EMS-induced mutants that had lost no DNA markers revealed mutation in one of the CC-NB-LRR orthologs of Mla. Transgenic complementation tests in stem rust susceptible wheat proved this gene to be Sr50. A survey of a set of rye accessions identified several carrying the gene but occurring in different Mla gene haplotypes based on DNA gel blot patterns and copy number of Mla orthologs. Several different powdery mildew and rust resistance genes including TmMla1 from T. monococcum, 23 Mla alleles from barley and stem rust resistance genes Sr33 from Aegilops tauschii and Sr50 from rye are all members of the Mla clade of cereal R genes. The gene Sr50,was initially thought to be allelic to Sr31, however, appearance of Ug99 showed that this is a different gene and is rye ortholog of barley Mla powdery mildew resistance gene. The cloning of Sr50 gives us an opportunity to screen the rye germplasm for presence of Sr50 and allows us to now do functional analysis of the various domains and understand the mechanism of resistance. The cloning also helps to add very effective resistance to gene cassette. Sr50 is effective against all the stem rust isolates around the globe
A new method for rapid generation advance, called ‘speed breeding’, has considerable advantages over DH technology for spring wheat because it provides increased recombination during line development and enables selection in early generations for some traits. The system has been refined over the past 8 years at The University of Queensland, utilizing controlled temperature regimes and 24-hour light to accelerate plant growth and development. The low-cost management system enables up to 6 plant generations of wheat annually – just like Arabidopsis. Currently, three of the six wheat breeding companies in Australia are exploiting speed breeding, and elite lines developed using the technology are in the final stages of yield evaluation. Recently, we developed methods adapted for use in the speed breeding system, which permit year-round high-throughput screening for adult plant resistance (APR) to rust pathogens that attack wheat. In this presentation, we describe the protocols, explain how phenotypes are related to field-based measures and highlight how the system can even handle diverse germplasm, such as winter types and landraces. Our ‘triple rust’ screening methodology enables selection for APR to all three rust pathogens and crossing of selected plants within a single plant generation. We applied the technique to rapidly introgress rust resistance into several Australian cereal cultivars. The technology is also a useful tool to accelerate rust research efforts. RIL populations designed for mapping novel APR genes can be developed within 12–18 months. Experiments to understand gene function in terms of temperature stability and onset of resistance can be performed year-round and if combined with sequencing technologies, such as RNAseq, transcripts involved in rust defence can be rapidly identified and harnessed via the speed breeding system. We will also reveal our current activities aiming to integrate the system with other plant breeding technologies to maximise genetic gain for wheat.
The identification of R-genes using traditional map-based approaches is a long, laborious process, not to mention the time required for subsequent development of cultivars incorporating the new resistances. Breeders seek to reduce the length of breeding cycles, and researchers require new tools to accelerate discovery and understanding of mechanisms associated with durable resistance, especially adult plant resistance (APR). A new method for rapid generation advancement, known as ‘speed breeding’, significantly reduces the length of breeding cycles, provide increased recombination during line development and enable selection in early generations. The speed breeding protocol uses controlled temperature regimes and 24h light to accelerate plant growth and development. Phenotyping methods adapted for use in the speed breeding system permit year-round evaluation of APR to rust pathogens within 5 weeks from time of sowing. RNA sequencing (RNA-Seq) technology has revolutionized gene expression profiling in plants. We previously used RNAseq to identify novel transcripts and miRNAs associated with seedling resistance (Lr28) leading to identification of transcription factors and miRNA families (e.g. miR36, miR37 and miR39) involved in signalling and defense response (Kumar et al. J. Nuc. Acids 2014:570176). In this study we report the application of speed breeding and RNAseq technologies for the purpose of rapidly identifying transcripts and miRNA associated with APR. Wheat landraces harbouring novel sources of resistance were grown under speed breeding conditions and sampled for RNA at key growth stages, before and after inoculation, which enabled discovery of differentially expressed miRNAs. Our next steps are aimed at validating these genetic factors associated with APR in order to better understand the signalling pathways and deliver tools to assist the assembly of robust wheat cultivars for the future.
To reduce losses caused by rusts, regular and timely replacement of susceptible varieties with new high yielding, rust resistant varieties must occur. Data from a farmer survey carried out across Pakistan (Punjab, Sindh, KPK and Baluchistan) in 2014 enabled an analysis of the uptake of rust resistant variety NARC 2011. The empirical results indicated that the major sources of information that farmers obtained about NARC 2011 were research stations (83%), seed companies (7%) and fellow farmers (5%). Although production inputs were applied equally to both rust resistant NARC 2011 and rust susceptible wheat varieties the average yield of NARC 2011 (5,063 kg/ha) was superior to high yielding but rust susceptible varieties (4,446 kg/ha). Quality attributes of NARC 2011, including taste, color, dough kneading and chapatti making properties, were preferred by >70% of farmers). Seed availability and accessibility of NARC 2011 were major issues. Farmer awareness of rusts, especially the threat of exotic Pgt race Ug99, needs to be improved.
A wheat genotype PBW343+Gpc-B1+LR24 containing the high grain protein content (GPC) gene Gpc-B1 linked to marker Xucw108 was used as the donor parent to transfer Gpc-B1 and Lr24 into Eastern Gangetic Plains (EGP) cv. HUW234 and HUW468 that were released in 1986 and 1999, respectively. The backcrossing program involved the following steps: (i) foreground selection, (ii) marker selection, and (iii) recovery of recipient parent genome. Grain protein contents were recorded for all selected plants from the BC2F2:3 generation. The dominant marker Xucw108 was used for foreground selection, and heterozygous plants were identified through progeny testing. For RPG recovery, both genotypic and phenotypic selection was used. Introgression of the high GPC gene into the recipient background without yield loss was completed in 5 years, starting from 2009-10 (F1) and completed in 2013-14 (BC2F5). A conventional selection program would take the same time to reach BC2F5 but ensuring the transfer of GPC would not not be possible. Ten selected single plants from the BC2F3:4 generation had comparable yields of the parents with 26% higher GPC than the recurrent parent HUW 234. Eight selected plants had comparable yields and 34% higher GPC than HUW 468. Multi-row progenies (BC2F4 and BC2F5) of each selected plant were evaluated in yield traits with the donor and recipient parents as controls during 2012-13 and 2013-14. Two lines based on each recurrent parent were identified with significantly higher GPC with no yield penalty. The study reinforced the belief that MAS in combination with phenotypic selection could be a useful strategy to develop high GPC genotypes without sacrificing grain yield. These lines will be submitted to national trial where MAS derived lines require only two years of testing compared to four years for conventionally bred lines.
Rusts and drought are the principal yield-limiting factors for wheat production in the Central Anatolian region of Turkey. The aim of the study was to determine resistance sources in a crossing block of drought tolerant lines. Seedling tests involving all three rusts were carried out at CRIFC, Yenimahalle, in 2014. Inoculations were made with local Pgt (avirulent on differentials with Sr24, Sr26, Sr27 and Sr31), Pt (avirulent on differentials with Lr9, Lr19, Lr24 and Lr28) and a local Pst population. Reactions were scored 14 days post-inoculation on 0-4 (LR and SR) or 0-9 (YR) scales. Seventeen (19%) genotypes were resistant to stripe rust, 11 (12%) were resistant to leaf rust, and 17 (19%) were resistant to stripe rust.
Bread wheat is the most important cereal crop in Turkey. Rusts (caused by Puccinia spp.) are the most significant diseases affecting wheat yield and quality on the Central Anatolian Plateau. The purpose of this study was to identify the reactions of 198 Turkish, white seeded, winter wheat genotypes developed by the Central Research Institute for Field Crops (CRIFC) and entered in preliminary yield trials. Adult plant and seedling tests were conducted for stripe rust whereas only seedling tests were conducted for leaf rust and stem rust. Evaluations were carried out at CRIFC, İkizce and Yenimahalle, in the 2014 season. For adult plant stripe rust assessments the materials were inoculated with a local Pst population (virulent on differentials carrying Yr2, Yr6, Yr7, Yr8, Yr9, Yr25, Yr27, YrSd, YrSu, and YrA). Stripe rust development on each entry was scored using the modified Cobb scale when the susceptible check Little Club had reached 80S in June 2014. Coefficients of infection were calculated and values below 20 were considered to be resistant. Seedlings were inoculated with local Pgt (avirulent on differentials with Sr24, Sr26, Sr27 and Sr31), Pt (avirulent on differentials with Lr9, Lr19, Lr24 and Lr28) and the Pst population. Reactions were scored for each entry at 14 days post-inoculation on standard 0-4 (LR and SR) or 0-9 (YR) scales. At the seedling stage, 56 (28%), 43 (22%), and 31 (31%) genotypes were resistant to SR, LR and YR, respectively. Eighty three (42%) lines were resistant to YR at the adult stage.
Northern Kazakhstan and Western Siberia are major high latitude spring wheat growing regions on the Eurasian continent. Rust epidemics can cause serious crop losses in this region. For this purpose, the Kazakhstan-Siberian network for wheat improvement (KASIB) was created in 2000. Seventy wheat cultivars and lines from a KASIB nursery were characterized for seedling and adult plant resistance (APR) to leaf rust using Australian pathotypes in greenhouse and field experiments. A molecular marker (STS iag95) detecting 1RS and therefore genes located in the rye component of the 1BL.1RS translocation was used to verify the presence/absence of Lr26. Field assessments of the nursery were conducted at Cobbitty using mixed Pt pathotypes. Lr26 was detected in five cultivars (Bayterek, GVK-1916-9, Altayskaya 105, Ok-1, and Omskaya 36) based on seedling tests using seven pathotypes. This was confirmed using the SRS marker. Other genes postulated included Lr3a (in cv. GVK 1860/8, GVK 1369/2, GVK 1857/9, and GVK 1526-2) and uncharacterized gene/s in cv. Zhenis and Lutescens-166 SP 94). The majority of KASIB entries were susceptible in seedling tests to Pt, but varying levels of potentially useful resistance were observed in 23 genotypes tested in the field. Low infection types on seedlings and field resistance in cv. Tertsia, Aria, and Sonata suggested the presence of unknown gene/s of potential value that warrant further investigation. Future efforts to breed wheat varieties resistant to one or more of the cereal rust pathogens will require identification of resistance sources that differ from those already present. Understanding the dynamics of pathogenic variability in pathogen populations is also important in selecting appropriate resistances.
CIMMYT wheat germplasm flow to Ethiopia started in the late 1960s. Over 90 bread wheat varieties were released over the decades. Of these, about 77% had CIMMYT origins or were derived from CIMMYT materials. Wheat is a traditional rainfed crop grown by 5 million small-scale farmers on 1.6 ha more or less. Yields have increased from 1.0 t/ha in the 1960s to 2.54 t/ha in 2014 mainly due to high yielding semi-dwarf bread wheat varieties and modern agronomic practices. Using such technologies, better farmers often get 5-6 t/ha. The rusts are the most important production constraints. For example, the 2010 yellow rust epidemic debilitated the mega varieties Kubsa and Galama in the highlands. In 2013/14, stem rust caused up to 100% yield losses in the widely adopted bread wheat variety Digalu in Arsi and Bale. This epidemic was caused by Pgt race TKTTF, which is virulent to the gene SrTmp that is present in Digalu, but is avirulent to Sr31, which is overcome by race Ug99 (TTKSK) and derivatives. To avert the increasing threat of rusts, CIMMYT developed a shuttle breeding program where germplasm moves back and forth between Mexico and Kenya and has increased nursery testing sites (Holetta, Kulumsa, Debre Zeit, Sinana, Adet, and Melkassa) in Ethiopia from two to six. The germplasm passes through rigorous tests against major diseases during both the main- and off-seasons. To obtain high yielding rust resistant germplasm, many hundreds of genotypes were introduced and tested over the last two years. In 2014/15, 266 (25%) lines with multiple disease resistances and high yield were promoted to national trials. CIMMYT continues to be an important source of germplasm. Fast tracked variety testing and release, accelerated seed multiplication, demonstration and popularization of new varieties with high yield, multiple disease resistance, and acceptable quality will continue.