International Wheat Breeding Research Articles

Cloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii

The wheat wild relative Aegilops tauschii was previously used to transfer the Lr42 leaf rust resistance gene into bread wheat. Lr42 confers resistance at both seedling and adult stages, and it is broadly effective against all leaf rust races tested to date. Lr42 has been used extensively in the CIMMYT international wheat breeding program with resulting cultivars deployed in several countries. Here, using a bulked segregant RNA-Seq (BSR-Seq) mapping strategy, we identify three candidate genes for Lr42. Overexpression of a nucleotide-binding site leucine-rich repeat (NLR) gene AET1Gv20040300 induces strong resistance to leaf rust in wheat and a mutation of the gene disrupted the resistance. The Lr42 resistance allele is rare in Ae. tauschii and likely arose from ectopic recombination. Cloning of Lr42 provides diagnostic markers and over 1000 CIMMYT wheat lines carrying Lr42 have been developed documenting its widespread use and impact in crop improvement.

A New Virulent Race of Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) on the Resistance Gene Yr5 in Turkey.

The gene Yr5 in wheat has generally been known to confer resistance to Puccinia striiformis f. sp. tritici races worldwide. However, a few reports indicated that some isolates of the stripe rust pathogen were virulent on the wheat genotypes with Yr5 in India, Australia, and China (Nagarajan 1986; Wellings and McIntosh 1990; Zhang et al. 2020). In April 2020, a stripe rust infection was observed on Triticum spelta 'Album' (TSA), the Yr5 donor, provided by Turkey Seed Gene Bank in a wheat breeding field at the experimental station of Akdeniz University in the Antalya province of Turkey. The sample was tested on the seedlings of the Yr single-gene lines in the Avocet S (AvS) background including Yr5 near-isogenic line (AvSYr5NIL), TSA, and susceptible bread wheat variety 'Morocco' according to the procedure reported by Wan et al. (2014), and found to be highly virulent on Morocco with infection type (IT) 9 and virulent on AvSYr5NIL and TSA with IT 7. To confirm this novel finding, single-pustule isolates derived from this sample were obtained from TSA and re-tested on the differentials and TSA. The Yr5-virulent isolate yielded similar infection types on these plants further verifying previous results. The single-pustule isolates were determined to be avirulent (Avr) (IT 0 to 6) on AvSYr1NIL, AvSYr8NIL, AvSYr9NIL, AvSYr10NIL, AvSYr32NIL, and AvSYr43NIL and virulent (Vr) (IT 7 to 9) on AvSYr5NIL, AvSYr6NIL, AvSYr7NIL, AvSYr17NIL, AvSYr24NIL, AvSYr27NIL, AvSYr44NIL, AvSYrSpNIL, and TSA. The isolates were identified as a new race and temporarily named TRVR20-5 based on its Avr/Vr pattern. Furthermore, to confirm the presence of Yr5, the genomic DNA of fresh leaves of AvSYr5NIL and TSA used in the virulence testing were isolated using NucleoSpin Plant II (Macherey-Nagel, Germany) according to the manufacturer's procedure. The genomic DNA samples were amplified with the primers STS-7 (5'-GTACAATTCACCTAGAGT-3') and STS-8 (5'-GCAAGTTTTCTCCCTATT-3') (Chen et al. 2003) using a thermal cycler (T-100, BioRad, USA), and the resulting PCR products were digested with DpnII and visualized on an agarose gel. AvSYr5NIL and TSA had the fragment linked to the resistance allele (308 bp) whereas AvS and Morocco had the fragment linked to the susceptible allele (181 bp). Thus, both wheat genotypes were confirmed to carry Yr5, and the new Pst race virulent to Yr5 was confirmed. To the best of our knowledge, this is the first report of a Pst race virulent to Yr5 in Turkey, where stripe rust epidemics have occured in 2 out of every 5 years with 1-5% crop losses in over 25% of the wheat growing areas (Chen 2020). In a nutshell, monitoring the Pst races virulent to Yr5 with a potential to cause devastating epidemics worldwide is crucial due to the fact that international wheat breeding programs have been using Yr5 to develop wheat cultivars with resistance to stripe rust.

Genetic Gains in Wheat Breeding and Its Role in Feeding the World

Wheat is the leading global food crop providing 19% of the daily calories and 21% of protein requirements for humans. The wheat production has increased from 220 million tons in 1961 to 750 million tons in 2018 with total production area of 220 million hectares which showed insignificant changes across years. The development of high yielding and widely adapted semi-dwarf input responsive wheat varieties, application of fertilizer, pesticides, irrigation, mechanization and implementation of favorable policies have contributed to such significant jump in wheat production at global level. The average annual genetic gain of wheat has been reported to be 1% while the demand for wheat increases by 1.7% annually reaching a total of 1 billion tons in 2050. To this end, conventional and molecular breeding strategies and approaches such as inter-country shuttle breeding, doubled haploid breeding, speed breeding, marker assisted selection, genomic selection, key location phenotyping and hybrid wheat breeding should be utilized intensively. The international wheat breeding programs at CIMMYT and ICARDA have developed and distributed germplasm to the world in the past 4 or more decades during which hundreds of high yielding and widely adapted wheat varieties with resistance tolerance to the major prevailing abiotic and biotic stresses have been released and adopted. Breeding progress or genetic gains in wheat has been determined by different authors with average relative gains reaching up to 2.5% per year. This paper reviews the global challenges facing demand and supply of wheat, the strategies to increase breeding efficiency and genetic gains, the impacts of the international wheat breeding and its progress, and future strategies to increase wheat production while conserving the natural resource base.

RNA interference targeting rye secalins alters flour protein composition in a wheat variety carrying a 1BL.1RS translocation

Wheat varieties carrying chromosome translocations from rye are part of the international wheat breeding pool despite being associated with defects in dough processing quality. One cause proposed for the quality defects of wheat carrying 1BL.1RS translocations is the presence of the secalins encoded by the Sec1 locus on the short arm of rye chromosome 1. In this report, we decrease the levels of these and related wheat proteins by RNA interference (RNAi). A plasmid designed to down-regulate secalin was introduced by biolistics into ‘Bobwhite’, which carries a 1BL.1RS translocation. Flour proteins of two independent transformants were analyzed in detail by 2-dimensional gel electrophoresis and tandem mass spectrometry. Compared to the parent, the transformants exhibited up to 5.5-fold decreases in the levels of individual secalins, up to 7-fold decreases in the closely related omega gliadins, and lesser decreases in many gamma gliadins, low-molecular-weight (LMW)-glutenins, and farinins. Increased levels were found for nearly all identified alpha gliadins, triticins, and y-type high-molecular-weight (HMW)-glutenins. Flour from the transgenic lines exhibited changes in dough mixing behavior in the 2-g mixograph, including longer development times and greater tolerance to mixing. We conclude that changes in protein composition engineered by this RNAi construct improved dough handling characteristics.

Evaluating Testing Strategies for Plant Breeding Field Trials: Redesigning a CIMMYT International Wheat Nursery

ABSTRACTGenotypes produced from plant breeding programs for annual crops are evaluated in multiyear, multilocation field trials where a large number of genotypes grown in a few locations in the first year are progressively reduced by selection and tested in a greater number of locations in successive years. Provided fixed resources are specified, the efficiencies of testing strategies differing in the number of locations and replications used and in the number of genotypes tested in successive years can be evaluated by three statistics (genetic repeatability, acceptance probability, and potential gain) calculated from five variance components applicable to the field trials. The five variance components required are deployed genetic variance, genotype‐by‐year, genotype‐by‐location, and genotype‐by‐year‐by‐location interaction variances and the residual (error) variance. Strictly, known variance components are required, but the statistics and their standard errors can be calculated using robust estimates of the variance components obtained from a combined analysis over years of a large set of historical data from field trials that are connected by shared genotypes across years, as genotype‐by‐year and genotype‐by‐year‐by‐location variance components are estimable. Single‐year analyses are unsuitable, as no estimate of the interactions with year are available, and such analyses produce biased estimates of genetic variance and genotype‐by‐location interaction variance. These procedures are illustrated using an example from the CIMMYT international wheat breeding program to evaluate 2‐yr testing strategies for CIMMYT's Elite Spring Wheat Yield Trials that has been distributed and evaluated internationally since 1979.

The use of unbalanced historical data for genomic selection in an international wheat breeding program

Genomic selection (GS) offers breeders the possibility of using historic data and unbalanced breeding trials to form training populations for predicting the performance of new lines. However, when using datasets that are unbalanced over time and space, there is increasing exposure to different genotype – environment combinations and interactions that may make predictions less accurate. Global cross-validated genomic prediction accuracies may be high when using large historic datasets but accuracies for individual years using a forward-prediction approach, or accuracies for individual locations, are often much lower. The objective of this study was to evaluate the overall accuracy of genomic predictions for untested genotypes using an unbalanced dataset to train a genomic selection model, and to explore ways of combining genomic selection and genotype-by-environment (G×E) interaction models to better target untested lines to different locations. Using the International Center for Maize and Wheat Improvement's (CIMMYT) Semi-Arid Wheat Yield Trials (SAWYT) we assessed the accuracy of genomic predictions and the potential to subset these nurseries using the concept of mega-environments (ME) adapted to a genomic selection context. We found that there was no difference in accuracy between models accounting for G×E interactions and global models. Data-driven methods of clustering locations based on similarities in genomic predictions also failed to improve accuracies within clusters. Using a simulation based on the empirical SAWYT data, we found that if there were different true genotypic values between clusters, there was an advantage to modeling G×E in prediction models. In the SAWYT dataset it appears that there is not a consistent pattern of genotype-by-environment interaction among the ME, and this dataset is not balanced enough to partition into new clusters that have predictive power.

Analysis of TaALMT1 traces the transmission of aluminum resistance in cultivated common wheat (Triticum aestivum L.)

Allele diversities of four markers specific to intron three, exon four and promoter regions of the aluminum (Al) resistance gene of wheat (Triticum aestivum L.) TaALMT1 were compared in 179 common wheat cultivars used in international wheat breeding programs. In wheat cultivars released during the last 93 years, six different promoter types were identified on the basis of allele size. A previous study showed that Al resistance was not associated with a particular coding allele for TaALMT1 but was correlated with blocks of repeated sequence upstream of the coding sequence. We verified the linkage between these promoter alleles and Al resistance in three doubled haploid and one intercross populations segregating for Al resistance. Molecular and pedigree analysis suggest that Al resistance in modern wheat germplasm is derived from several independent sources. Analysis of a population of 278 landraces and subspecies of wheat showed that most of the promoter alleles associated with Al resistance pre-existed in Europe, the Middle East and Asia prior to dispersal of cultivated germplasm around the world. Furthermore, several new promoter alleles were identified among the landraces surveyed. The TaALMT1 promoter alleles found within the spelt wheats were consistent with the hypothesis that these spelts arose on several independent occasions from hybridisations between non-free-threshing tetraploid wheats and Al-resistant hexaploid bread wheats. The strong correlation between Al resistance and Al-stimulated malate efflux from the root apices of 49 diverse wheat genotypes examined was consistent with the previous finding that Al resistance in wheat is conditioned primarily by malate efflux. These results demonstrate that the markers based on intron, exon and promoter regions of TaALMT1 can trace the inheritance of the Al resistance locus within wheat pedigrees and track Al resistance in breeding programmes.

Challenges to international wheat breeding

Challenges to international wheat breeding

Sixty-two years of fighting hunger: personal recollections

International wheat breeding began 60 years ago in the Mexican-Rockefeller Foundation Office of Special Studies. A novel technique of shuttle breeding was adopted in Mexico, enabling photoperiod sensitivity to be overcome, a pivotal step in creating internationally adapted spring wheat germplasm that eventually spread throughout the world. The high-yielding technologies developed in Mexico helped revolutionize cereal production during the 1960s and 1970s, and came to be known as the “Green Revolution.” In the process, a highly effective system of international agricultural research centers evolved under the umbrella of the Consultative Group for International Agriculture (CGIAR). This international system has weakened in recent decades, despite the enormous challenges facing humankind to expand food production in environmentally sustainable ways. Biotechnology holds great promise to develop improved crop varieties to deal with new pests and diseases, drought, and to enhance nutritional content. Those on the food front still have a big job ahead of us to feed the world. There is no room for complacency.

Impacts of breeding on international collaborative wheat improvement

For over 40 years a collaborative network of publicly funded international wheat scientists has made a significant contribution to food security in the developing world. Thousands of modern wheat varieties (MVs) have been released for use in both favourable and marginal environments on well over 50 million hectares. The yield increases associated with genetic improvement in yield potential and adaptation to biotic and abiotic stresses are well documented. Millions of small-scale farmers in the developing world have benefited. While this so-called ‘Green Revolution’ displaced landraces in favour of more productive MVs, these and other genetic resources, held in trust by international organizations, have been utilized to improve the inherent genetic diversity of modern varieties. Furthermore, the result of increased yields reduced the need to bring natural ecosystems under cultivation, by as much as a billion hectares.Although international wheat breeding has its origins in the 1940s, recognition of a common scientific basis of agricultural problems worldwide was highlighted by the creation of International Agricultural Research Centres (IARCs) which included the International Maize and Wheat Improvement Centre (CIMMYT) established in 1965. This grew into a larger network called the Consultative Group for International Agricultural Research (CGIAR) now comprising 15 IARCs, including the International Centre for Agricultural Research in the Dry Areas (ICARDA) established in Syria in 1977, another key player in the international wheat and barley breeding network. Two of the major coordination responsibilities of CIMMYT are maintaining the world collection of wheat genetic resources – a public good protected by international treaty – and the facilitation of the International Wheat Nurseries.After the initial impact of the Green Revolution in high production zones through exploitation of Rht-B1 and Rht-D1 dwarfing genes in conjunction with disease resistance, international breeding encompassed more challenging environments through, for example, international shuttle breeding between Brazil and Mexico to overcome problems associated with acid soils that restricted adoption of MVs. Another example is drought, which affects at least 30 million ha of wheat in the developing world. The approach focused initially on exploiting the inherent yield potential and disease resistance of MVs and later combined this with new stress-adaptive traits from wild wheat ancestors through wide crossing techniques. Adoption of modern varieties has increased substantially in drier areas between 1990 and 1997. In all environments, possibly the greatest threat to productivity is disease, especially those caused by fungal pathogens. International wheat breeding has placed great emphasis on genetic control of disease since resource-poor farmers generally lack the means to control diseases chemically.

Editorial

In our Editorial in the first issue of 2005 (Naylor & Wiseman 2005), we celebrated the Journal's achievement of 100 years of publication and introduced the Centenary Reviews. We have been gratified at the interest in the Centenary Reviews and the willingness of authors to consider writing them. This, coupled with the observation that the first volume of the Journal of Agricultural Science was 1905–06, has enabled us to continue the series of Centenary Reviews into the 2006 volume. We thank the various authors for their time and effort in writing these reviews. In 2006 we anticipate Centenary Reviews on international wheat breeding, crop losses, lentils, yield forecasting and grapevine evolution, amongst others.

Impacts of international wheat breeding research in the developing world, 1988-2002

The third in a series of global studies, this report (covering 1988-2002) documents the adoption and diffusion of modern wheat varieties in the developing world and assesses the benefi ts generated by international wheat breeding efforts. It updates the fi ndings and confi rms the three major conclusions of the two earlier studies, and extends the coverage to include many countries in Eastern Europe and the former Soviet Union. In the postGreen Revolution era, CIMMYT’s improved germplasm continues to be used extensively by breeding programs in developing countries, and public investment in international wheat breeding research continues to generate high rates of return. Measured in terms of varietal releases, wheat breeding programs in developing countries continue to be very productive. Between 1988 and 2002, public national research organizations and private seed companies in the developing world released nearly 1,700 wheat varieties. The international wheat breeding system continues to be dominated by public breeding programs, but private companies also engage in wheat breeding in a number of developing countries. More than 75% of protected cultivars (those with plant breeding rights) in South America have CIMMYT ancestry. Of the area planted to wheat in the surveyed countries, 64% was sown to varieties containing CIMMYT-related germplasm, and 24% of varieties in those countries were derived from CIMMYT crosses. A simple economic surplus model was used to estimate the value of additional grain production attributable to the adoption of modern wheat varieties in developing countries. Depending on the stringency of the method used, the value of additional grain ranges from US$ 2.0 to 6.1 billion per year (2002 dollars). The extensive use of CIMMYT germplasm by public and private breeding programs, combined with the widespread adoption of CIMMYT-derived varieties, generates signifi cant benefi ts. Using the most conservative rule for attributing credit to CIMMYT (CIMMYT cross), the annual benefi ts associated with the use of CIMMYT-derived germplasm range from US$ 0.5 to 1.5 billion (2002 dollars), a huge return on CIMMYT’s annual investment (US$ 9-11 million in 2002 dollars) in wheat improvement research.

International wheat breeding research in Eastern and Southern Africa, 1966-97

This paper describes and analyzes some of the impacts of wheat improvement research in seven countries in the Eastern and Southern regions of Africa. The countries—South Africa, Ethiopia, Sudan, Kenya, Zimbabwe, Tanzania, and Zambia—produce nearly 99% of all the wheat grown in the region and 97% of all wheat grown in sub-Saharan Africa. The first section of the paper is a brief review of wheat production in the region, concentrating on production levels and growing environments. The second section analyzes the wheat improvement research effort. The third section looks at the pattern of release of wheat varieties over time, as well as the use of wheat germplasm from CIMMYT. The fourth section presents data about varieties that are currently grown in farmers' fields. The fifth section considers some of the organizational issues involved in making wheat breeding research more efficient. The paper concludes that many of the wheat improvement research programs in Eastern and Southern Africa have been successful. However, the small amount of wheat produced in many countries raises the question of whether the same results could have been obtained at lower cost through greater efficiencies in research organization and even greater reliance on research spill-ins.

Approaches for breaching yield stagnation in wheat

This paper outlines the breeding objectives, methodology, and genetic gains of the international wheat breeding program of the International Maize and Wheat Improvement Center (CIMMYT) based in Mexico. The historical analysis of yield gains asserts that wise use of genetic diversity has been paramount in raising the yield ceiling and expanding genetic variability. Data is provided to support a philosophical view that yield potential per se should be combined with both abiotic and biotic tolerances in the breeding of future cultivars. The erosion of high yield potential should be avoided at all costs through a protective shield of wide-spectrum disease resistance genes.Key words: yield potential, shuttle breeding, Aegilops squarrosa.