Wheat breeding assisted by markers: CIMMYT’s experience

Significant progress has been made in the characterization of loci controlling traits of importance using molecular markers. A number of markers are currently available in wheat for genes of interest to the breeders. Markers can be used to better characterize parental material, thereby improving the efficiency and effectiveness of parental selection for crossing and to track genes in segregating progenies through the selection process. Although a number of breeding programs are using molecular markers at modest levels, the costs associated with marker assisted selection (MAS) are frequently cited as the main constraint to their wide-spread use by plant breeders. However, this is likely to change when user-friendly, high-throughput, automated marker technologies based on single nucleotide polymorphisms become available. These evolving technologies will increase the number of available markers, and will improve the efficiency, throughput, and cost effectiveness of MAS, thereby making it more attractive and affordable to many breeding programs. This article examines the extent to which molecular markers have been used at the International Maize and Wheat Improvement Center (CIMMYT) in applied wheat breeding and reviews the limited publicly available information on MAS from other wheat breeding programs. As markers are currently available for relatively few traits, we believe that MAS must be integrated with ongoing conventional breeding to maximize its impact. When used in tandem with phenotypic selection, MAS will improve response to selection for certain traits, thereby increasing rates of genetic progress.     

Application of new knowledge,technologies, and strategies to wheat improvement

There have been many changes impacting wheat improvement since the 1996 International Maize and Wheat Improvement Center Wheat Yield Symposium. This review highlights a few of the technological advances and impacts of new knowledge on wheat improvement that have occurred in the past 10 years as well as on-going challenges. One of the most dramatic discoveries has been the revelation that the genomes of graminaceous crops are complex, rapidly evolving, and heterogeneous, even within species. The use of marker-assisted selection for improving complex traits is one of the challenges facing wheat breeders. Integration of association analysis into conventional breeding programs is proposed as a crop improvement strategy that has the potential to improve the efficiency of molecular breeding.     

Participatory plant breeding research: Opportunities and challenges for the international crop improvement system

This paper describes the current state of international plant breeding research and explains why the centralized global approach to germplasm improvement that was so successful in the past is today being transformed by the incorporation of decentralized local breeding methods designed to better incorporate the perspective of end users into the varietal development process. It describes international breeding efforts for major crops and identifies factors that have contributed to the success of the international breeding system; discusses shortcomings of the global approach to plant breeding and explains why future successes will depend critically on researchers' ability to incorporate the knowledge and preferences of technology users; reviews a number of farmer participatory research methods that are currently being tested by plant breeding programs throughout the developing world; describes synergies that can potentially be achieved by linking centralized global and decentralized local breeding models; and discusses technical, economic, and institutional challenges that will have to be overcome to integrate end user-based participatory approaches into the international plant breeding system. This revised version was published online in August 2006 with corrections to the Cover Date.     

Should spring wheat breeding for organically managed systems be conducted on organically managed land?

Organic spring wheat (Triticum aestivum L.) producers in the northern Great Plains use cultivars which have been bred for conventional management systems or heritage cultivars released before the widespread use of synthetic fertilizers and pesticides. To investigate the feasibility of organic wheat breeding and to determine common genetic parameters for each system, we used a random population of 79 F₆-derived recombinant inbred sister lines from a cross between the Canadian hard red spring wheat cultivar AC Barrie and the CIMMYT derived cultivar Attila. The population, including the parents, was grown on conventionally and organically managed land for 3 years. Heritability estimates differed between systems for 6 of the 14 traits measured, including spikes m⁻², plant height, test weight, 1,000 kernel weight, grain protein, and days to anthesis. Direct selection in each management system (10% selection intensity) resulted in 50% or fewer lines selected in common for nine traits, including grain yield, grain protein, spikes m⁻², and grain fill duration. The results of this study suggest that indirect selection (in conventionally managed trials) of spring wheat destined for organically managed production would not result in the advance of the best possible lines in a breeding program. This implies that breeding spring wheat specific to organic agriculture should be conducted on organically managed land.     

Breeding for low input conditions and consequences for participatory plant breeding examples from tropical maize and wheat

Participatory plant breeding (PPB) has been suggested as an effective alternative to formal plant breeding (FPB) as a breeding strategy for achieving productivity gains under low input conditions. With genetic progress through PPB and FPB being determined by the same genetic variables, the likelihood of success of PPB approaches applied in low input target conditions was analyzed using two case studies from FPB that have resulted in significant productivity gains under low input conditions: (1) breeding tropical maize for low input conditions by CIMMYT, and (2) breeding of spring wheat for the highly variable low input rainfed farming systems in Australia. In both cases, genetic improvement was an outcome of long-term investment in a sustained research effort aimed at understanding the detail of the important environmental constraints to productivity and the plant requirements for improved adaptation to the identified constraints, followed up by the design and continued evaluation of efficient breeding strategies. The breeding strategies used differed between the two case studies but were consistent in their attention to the key determinants of response to selection: (1) ensuring adequate sources of genetic variation and high selection pressures for the important traits at all stages of the breeding program, (2) use of experimental procedures to achieve high levels of heritability in the breeding trials, and (3) testing strategies that achieved a high genetic correlation between performance of germplasm in the breeding trials and under on-farm conditions. The implications of the outcomes from these FPB case studies for realizing the positive motivations for adopting PPB strategies are discussed with particular reference for low input target environment conditions. This revised version was published online in August 2006 with corrections to the Cover Date.     

Breeding crops for reduced-tillage management in the intensive, rice–wheat systems of South Asia

The importance of reduced tillage in sustainable agriculture is well recognized. Reduced-tillage practices (which may or may not involve retention of crop residues) and their effects differ from those of conventional tillage in several ways: soil physical properties; shifts in host–weed competition; soil moisture availability (especially when sowing deeply or under stubble); and the emergence of pathogen populations that survive on crop residues. There may be a need for genotypes suited to special forms of mechanization (e.g. direct seeding into residues) and to agronomic conditions such as allelopathy, as well as specific issues relating to problem soils. This article examines issues and breeding targets for researchers who seek to improve crops for reduced-tillage systems. Most of the examples used pertain to wheat, but we also refer to other crops. Our primary claim is that new breeding initiatives are needed to introgress favourable traits into wheat and other crops in areas where reduced or zero-tillage is being adopted. Key traits include faster emergence, faster decomposition, and the ability to germinate when deep seeded (so that crops compete with weeds and use available moisture more efficiently). Enhancement of resistance to new pathogens and insect pests surviving on crop residues must also be given attention. In addition to focusing on new traits, breeders need to assess germplasm and breeding populations under reduced tillage. Farmer participatory approaches can also enhance the effectiveness of cultivar development and selection in environments where farmers’ links with technology providers are weak. Finally, modern breeding tools may also play a substantial role in future efforts to develop adapted crop genotypes for reduced tillage.     

Crop breeding for salt tolerance in the era of molecular markers and marker‐assisted selection

Crop salt tolerance (ST) is a complex trait affected by numerous genetic and non‐genetic factors, and its improvement via conventional breeding has been slow. Recent advancements in biotechnology have led to the development of more efficient selection tools to substitute phenotype‐based selection systems. Molecular markers associated with genes or quantitative trait loci (QTLs) affecting important traits are identified, which could be used as indirect selection criteria to improve breeding efficiency via marker‐assisted selection (MAS). While the use of MAS for manipulating simple traits has been streamlined in many plant breeding programmes, MAS for improving complex traits seems to be at infancy stage. Numerous QTLs have been reported for ST in different crop species; however, few commercial cultivars or breeding lines with improved ST have been developed via MAS. We review genes and QTLs identified with positive effects on ST in different plant species and discuss the prospects for developing crop ST via MAS. With the current advances in marker technology and a better handling of genotype by environment interaction effects, the utility of MAS for breeding for ST will gain momentum.     

Achievements and limitations of contemporary common bean breeding using conventional and molecular approaches

Common bean (Phaseolus vulgaris L.) improvement programs have been successful using conventional breeding methods to accomplish a wide array of important objectives. Specific achievements include the extension of range of adaptation of the crop, the development of cultivars with enhanced levels of disease and pest resistance and breeding lines that possess greater tolerance to drought. The most effective breeding method depends on the expression and inheritance of the trait to be selected and the target environment. Many bean improvement programs use molecular markers to facilitate cultivar development. In fact, several recent germplasm releases have used molecular markers to introgress and or pyramid major genes and QTL for disease resistance. Related species (P. coccineus and P. acultifolius) via interspecific hybridizations remain an important albeit long-term source for resistance to economically important diseases. Slow progress has been made in the improvement of traits such as adaptation to low soil fertility and tolerance to high levels of soluble Al in the soil using conventional breeding methods. The inability to directly measure root traits and the importance of genotype × environment interaction complicate the selection of these traits. In addition, symbiotic relationships with Rhizobium and mycorrhiza need to be taken into consideration when selecting for enhanced biological N fixation and greater or more efficient acquisition of soil P. Genomic examination of complex traits such as these should help bean breeders devise more effective selection strategies. As integration of genomics in plant breeding advances, the challenge will be to develop molecular tools that also benefit breeding programs in developing countries. Transgenic breeding methods for bean improvement are not well defined, nor efficient, as beans are recalcitrant to regeneration from cell cultures. Moreover, if issues related to consumer acceptance of GMOs cannot be resolved, traits such as herbicide tolerance in transgenic bean cultivars which would help farmers reduce production costs and decrease soil erosion will remain unrealized.     

A non-invasive crop ideotype to reduce invasive potential

Summary In plant breeding programs, qualitative and quantitative traits confer market value and, thus, constitute the basis for developing breeding criteria during crop domestication. Some traits such as high male/female fertility are advantageous in the wild and could enable the evolution of cultivated crops into invasive weeds. Other traits, e.g. sterility, are not expected to confer invasiveness. To date there has been very limited involvement in invasion risk assessment by plant breeders. Thus, in this paper we propose that trait-based selection of potential crop species be coupled with species design in the creation of a “non-invasive crop ideotype” as an avenue to reduce invasiveness during domestication. The non-invasive crop ideotype embodies the ideal characteristics for a crop to excel in cultivated environment(s) but minimizes the likelihood it will establish and spread in non-cultivated environments, constituting the underlying foundation for all breeding objectives, choice(s) of breeding methodologies, and propagation techniques for non-invasive crop release. Using ornamental (floriculture) horticultural crops as an example, we identify 10 traits to be used individually or in combination to reduce invasiveness while retaining commercial value: reduced genetic variation in propagules, slowed growth rates, non-flowering, elimination of asexual propagules, lack of pollinator rewards, non-shattering seed, non-fleshy fruits, lack of seed germination, sterility, and programmed death (apotopsis). A non-invasive crop ideotype would constitute the underlying foundation for all breeding objectives, the choice(s) of breeding methodologies, and propagation technique(s). The ideotype should be flexible and should adjust to species- and crop-specific traits to account for the intended use. For example, development of sterile cultivars may have negligible effects in reducing invasiveness if the crops spread vegetatively. A non-invasive crop ideotype may increase the direct participation of plant breeders, who are the professionals directly involved in the collection, development and release of new crops, in reducing the invasive potential of ornamental crops. Future research is required to determine the feasibility of incorporating each trait into various crops, use of classical or molecular techniques for creation of non-invasive crops, trait stability (lack of genotype × environment interaction over years and locations), consumer acceptance, and long-term viability.     

Plant traits related to yield of wheat in early, late, or continuous drought conditions

Bread wheats (Triticum aestivum L.) were evaluated for plant characteristics contributing to grain yield and plant adaptation under various drought patterns. The usefulness of these traits as explicit selection criteria in developing drought tolerant wheat varieties was investigated in three experiments. Cultivars from four germplasm groups, representing the four relevant major and distinct global wheat growing environments, were grown under the respective simulated early, late, continuous and no drought conditions by manipulating irrigation in north western Mexico. Additionally, 560 advanced lines from the CIMMYT breeding program were grown under late drought conditions, and 16 randomly selected advanced genotypes were studied in more detail under late and no drought conditions. In these three studies, the association between yield in drought-stressed environments and yield in non drought-stressed environments was interpreted to reflect genotypic high yield potential, mainly by way of high biomass development. However, yield potential only partly explained the superior performance under drought. For each pattern of drought stress, particular and often different plant traits were identified that further contributed specific adaptation to the distinct drought stress conditions. Knowledge of these traits will be useful for developing CIMMYT germplasm for specific drought-stressed areas. Ultimately, these studies demonstrate that both yield potential and specific adaptation traits are useful criteria in breeding for drought environments, and should be combined to achieve optimum performance and adaptation to drought stress. This revised version was published online in August 2006 with corrections to the Cover Date.     

Double haploids,markers and QTL analysis in vegetable brassicas

Double haploid (DH) plants of Brassica spp. can be produced via anther culture or culture of microspores. This paper reviews the uses of double haploids in crop improvement research in vegetable brassicas (B. oleracea). Applications of DH lines are described for breeding; construction of linkage maps; genetic analysis of quantitative traits and capturing genetic variation. The advantages and disadvantages of DH lines are discussed     

Lessons learnt from forty years of international spring bread wheat trials

Yield potential is the maximum attainable yield within the limits imposed by the production environment. Better understanding of these constraints and the underlying causes of genotype × environment interaction will improve productivity regionally and globally. For 40 years, the International Maize and Wheat Improvement Center (CIMMYT) has distributed wheat yield trials, and collaborators from across the world have provided yield, disease, and agronomic data. Various analyzes of these data have been conducted over the years to assess the effectiveness of CIMMYT’s Mexican based breeding program, and to identify key selection environments and genotypes with broad adaptation. Analysis of these data confirmed the value of shuttle breeding in Mexico. Well-watered and terminal heat stress selection environments generated in Mexico associate well with their global target areas. Germplasm targeting dry areas is selected and screened for drought tolerance in Mexico using limited irrigation. This type of screening correlated well with environments in South Asia, but less so with sites in West Asia and South America. On the basis of these findings, drought screening in Mexico has been modified to better reflect a wider array of drier environments. In contrast, CIMMYT’s high rainfall environment at Toluca, the other arm of the Mexico-based shuttle, was found to be a poor predictor of global high rainfall areas. The analysis of these data led to the identification of key locations in countries outside Mexico. Integrating information from these sites with that obtained in Mexico has helped improve the efficiency of CIMMYT’s global wheat breeding effort.     

Number of crosses and population size for participatory and classical plant breeding

In the breeding of self-pollinating crops, crossing creates variation upon which selection is exerted. If the value of crosses cannot be predicted then this uncertainty means that many crosses need to be made. However, since there is a limit to the capacity of a breeding programme, more numerous crosses result in each cross having a small population size, fewer progenies in later generations and a lower probability of recovering good genotypes from each cross. Published theory on the optimum number of crosses in a plant breeding programme, for a predominantly self-pollinating crop, usually assumes that all crosses are equal value. This overestimates the number of crosses required. When the optimum size of a population in a favourable cross is considered, theory predicts that very large populations are desirable. The required population size is even larger if linkage of loci controlling different traits is also considered. Hence, in an inbreeding crop, one possible strategy is to select a small number of crosses that are considered favourable and produce large populations from them to increase the probability of recovering superior genotypes. In an out breeding crop, the analogy is a few composites with large population sizes. This low-cross-number strategy is ideally suited to the particular constraints and advantages of participatory plant breeding. Such an approach, although not essential, may still be advantageous in classical breeding. When a breeding programme is based on few crosses, which parents are chosen is crucial and farmer participatory methods are highly effective in narrowing the choice. Modified bulk population breeding methods, and recurrent selection are desirable strategies in the participatory plant breeding of self-pollinating crops when combined with a low-cross-number approach. This revised version was published online in August 2006 with corrections to the Cover Date.     

中国作物分子育种现状与展望

分子育种是现代农业发展应用推广最迅速的育种新技术,对作物遗传改良产生了深远的影响。国际农作物育种已经进入分子育种时代,以DNA重组技术和基因组编辑技术等为代表的现代生物技术已成为世界上作物遗传改良的重要手段。本综述简要介绍了国际分子育种发展趋势,并对中国作物分子育种现状和国家相关政策导向、集成创新、科研管理体制、生物种业发展和人才现状等方面进行了分析,以期为中国农业和科技管理部门、生物技术工作者、育种家和种子企业提供参考。     

Characterization of Chinese wheat germplasm for resistance to Fusarium head blight at CIMMYT, Mexico

Fusarium head blight (FHB) poses a challenge for wheat breeders worldwide; there are limited sources of resistance and the genetic basis for resistance is not well understood. In the mid-1980s, a shuttle breeding and germplasm exchange program launched between CIMMYT-Mexico and China, enabled the incorporation of FHB resistance from Chinese bread wheat germplasm into CIMMYT wheat. Most of the Chinese wheat materials conserved in the CIMMYT germplasm bank had not been fully characterized for FHB reaction under Mexican environments, until 2009, when 491 Chinese bread wheat lines were evaluated in a FHB screening nursery in Mexico, and 304 (61.9 %) showed FHB indices below 10 %. Subsequent testing occurred in 2010 for plant height (PH), days to heading (DH), and leaf rust response. In 2012, 140 elite lines with good agronomic types were further evaluated for field FHB reaction and deoxynivalenol (DON) accumulation. Most of the tested lines showed good resistance: 116 (82.9 %) entries displayed FHB indices lower than 10 %, while 89 (63.6 %) had DON contents lower than 1.0 ppm. Significant negative correlations were observed between FHB traits (FHB index, DON content, and Fusarium damaged kernels) and PH, DH, and anther extrusion. A subset of 102 elite entries was selected for haplotyping using markers linked to 10 well known FHB quantitative trait loci (QTL). 57 % of the lines possessed the same 2DL QTL marker alleles as Wuhan 1 or CJ 9306, and 26.5 % had the same 3BS QTL allele as Sumai 3. The remaining known QTL were of low frequency. These materials, especially those with none of the above tested resistance QTL (26.5 %), could be used in breeding programs as new resistance sources possessing novel genes for FHB resistance and DON tolerance.     

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.     

小麦种质资源农艺性状变异及其遗传多样性分析

为了解不同小麦种质资源农艺性状变异及其遗传多样性,利用SSR分子标记分析了44份CIMMYT春小麦和45份国内主栽小麦种质资源的遗传变异。结果表明,小麦单株产量、株高和穗粒数的变异系数分别为36.7%、16.4%和15.6%,说明国内外种质材料在表型上存在较大差异。利用20对分子标记对89份小麦种质资源进行了多态性检测,结果显示,共检测到162个等位变异,每对引物检测到等位变异数目为6~9个,平均每对SSR标记能够检测到8.1个变异,其中Xgwm314的多态性最丰富;SSR标记的多态性信息含量（PIC）介于0.0223~0.8177,平均值为0.5109;平均每位点的有效等位基因数的变异范围为0.2984~8.7818,Xgwm165的多态性最丰富,平均值为1.2215;Shannon’s信息指数的变异范围为0.1114~0.3162,平均值为0.2307。聚类分析结果显示,89份小麦种质资源分为2大类群,第一类有25份,该类群株高较低,第二类有64份,国外材料大多集中在这一类中。本研究表明,44份CIMMYT春小麦及45份国内主栽小麦种质资源遗传相似性较大,地域性分布特征显著,聚类结果反映出小麦品种（系）多样性水平复杂,可为小麦新品种选育提供优异的亲本材料。     

Allelic changes in bread wheat cultivars were associated with long-term wheat trait improvements

Genetic impacts under selective breeding of agricultural crops have been frequently investigated with molecular tools, but inadequate attention has been paid to assess genetic changes under long-term genetic improvement of plant traits. Here we analyzed allelic changes with respect to wheat trait improvement in 78 Canadian hard red spring wheat cultivars released from 1845 to 2004 and screened with 370 mapped SSR markers. The improvements in quality, maturity, yield, disease, stem rust, leaf rust, sawfly resistance, and agronomy were considered. A total of 154 (out of 370) loci with significant allelic changes across 21 chromosomes were detected in the 78 wheat cultivars separated into improved versus non-improved groups for eight traits. The number of significant loci for improving a trait ranged from four for quality to 68 for yield and averaged 35. Many more loci with significant allelic reduction for improving a trait were detected than those with significant allelic increase. Selection for early maturity introduced more alleles, but improving the other traits purged more alleles. Significantly lower numbers of unique alleles were found in the cultivars with improved traits. The distributions of unique allele counts also varied greatly across the 21 chromosomes with respect to trait improvement. Significant SSR variation between two cultivar groups was observed for improvement in seven traits, but not in stem rust. The proportional SSR variation residing between two groups ranged from 0.014 to 0.118. The proportional SSR variations within the improved cultivar groups consistently were much lower than those within the non-improved groups. These findings clearly demonstrate the association between allelic changes and wheat trait improvements and are useful for understanding the genetic modification of the wheat genome by long-term wheat breeding.