Richard Trethowan

Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure

Linkage disequilibrium can be used for identifying associations between traits of interest and genetic markers. This study used mapped diversity array technology (DArT) markers to find associations with resistance to stem rust, leaf rust, yellow rust, and powdery mildew, plus grain yield in five historical wheat international multienvironment trials from the International Maize and Wheat Improvement Center (CIMMYT). Two linear mixed models were used to assess marker–trait associations incorporating information on population structure and covariance between relatives. An integrated map containing 813 DArT markers and 831 other markers was constructed. Several linkage disequilibrium clusters bearing multiple host plant resistance genes were found. Most of the associated markers were found in genomic regions where previous reports had found genes or quantitative trait loci (QTL) influencing the same traits, providing an independent validation of this approach. In addition, many new chromosome regions for disease resistance and grain yield were identified in the wheat genome. Phenotyping across up to 60 environments and years allowed modeling of genotype × environment interaction, thereby making possible the identification of markers contributing to both additive and additive × additive interaction effects of traits.

Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops

Drought is one of the most serious production constraint for world agriculture and is projected to worsen with anticipated climate change. Inter-disciplinary scientists have been trying to understand and dissect the mechanisms of plant tolerance to drought stress using a variety of approaches; however, success has been limited. Modern genomics and genetic approaches coupled with advances in precise phenotyping and breeding methodologies are expected to more effectively unravel the genes and metabolic pathways that confer drought tolerance in crops. This article discusses the most recent advances in plant physiology for precision phenotyping of drought response, a vital step before implementing the genetic and molecular-physiological strategies to unravel the complex multilayered drought tolerance mechanism and further exploration using molecular breeding approaches for crop improvement. Emphasis has been given to molecular dissection of drought tolerance by QTL or gene discovery through linkage and association mapping, QTL cloning, candidate gene identification, transcriptomics and functional genomics. Molecular breeding approaches such as marker-assisted backcrossing, marker-assisted recurrent selection and genome-wide selection have been suggested to be integrated in crop improvement strategies to develop drought-tolerant cultivars that will enhance food security in the context of a changing and more variable climate.

Bringing wild relatives back into the family: recovering genetic diversity in CIMMYT improved wheat germplasm

SummaryThe dangers of a narrow genetic base of the worlds major domesticated food crops have become a great global concern in recent decades. The efforts of the International Maize and Wheat Improvement Center (CIMMYT) to breed common wheat cultivars for resource poor farmers in the developing world (known as the Green Revolution wheats) has met with notable success in terms of improved yield, yield stability, increased disease resistance and utilization efficiency of agricultural inputs. However, much of the success was bought at the cost of an overall reduction in genetic diversity in the species; average Modified Rogers distances (MRD) within groups of germplasm fell from 0.64 in the landraces to a low of 0.58 in the improved lines in the 1980s. Recent efforts by CIMMYT breeders to expand the genetic base of common wheat has included the use of landraces, materials from other breeding programs, and synthetic wheats derived from wild species in the pedigrees of new advanced materials. The result, measured using SSR molecular markers, is a highly significant increase in the latent genetic diversity of recently developed CIMMYT breeding lines and cultivars compared to the original Green Revolution wheats (average MRD of the latest materials (0.63) is not significantly different from that of the landraces, as tested using confidence intervals). At the same time, yield and resistance to biotic and abiotic stresses, and end-use quality continue to increase, indicating that the Green Revolution continues to this day.

Evaluation of selection strategies for wheat adaptation across water regimes

Drought frequently constrains production of wheat (Triticum aestivum L.), but development of tolerant cultivars is hampered by low heritability for drought tolerance and a lack of effective selection strategies. Our objective was to identify an optimum selection regime for wheat in drought-prone environments. Six-hundred entries derived from 10 crosses were developed by selection under continuous high moisture, alternating high with low moisture, alternating low with high moisture, and continuous low moisture conditions for five generations. The selections were evaluated in two low-yield, a medium-yield, and a high-yield environment in the Yaqui Valley, Sonora, Mexico. The mean performance of entries derived from a particular selection regime was dependant on the stress level of the evaluation environment. Lines developed and selected under continuous high moisture and continuous low-moisture regimes produced the highest mean yields in the low moisture evaluation environment. There was no relationship between continuous selection under either high yielding conditions or low yielding conditions and the mean performance of the resultant lines in their respective high and low yielding evaluation environments. The mean yield of lines selected using the alternating high/low moisture regime as well as the five highest yielding lines were superior in the HY environment, and had similar performance with other regimes under the low yielding evaluation environment. Our results indicate that alternating selection between high and low yielding environments is the most effective way to develop wheat germplasm adapted to environments where intermittent drought occurs.

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 germ-plasm 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.

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.

Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.)

Water is essential for all living organisms. Aquaporin proteins are the major facilitator of water transport activity through cell membranes of plants including soybean. These proteins are diverse in plants and belong to a large major intrinsic (MIP) protein family. In higher plants, MIPs are classified into five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). This paper reports genome wide assembly of soybean MIPs, their functional prediction and expression analysis. Using a bioinformatic homology search, 66 GmMIPs were identified in the soybean genome. Phylogenetic analysis of amino acid sequences of GmMIPs divided the large and highly similar multi-gene family into 5 subfamilies: GmPIPs, GmTIPs, GmNIPs, GmSIPs and GmXIPs. GmPIPs consisted of 22 genes and GmTIPs 23, which showed high sequence similarity within subfamilies. GmNIPs contained 13 and GmSIPs 6 members which were diverse. In addition, we also identified a two member GmXIP, a distinct 5th subfamily. GmMIPs were further classified into twelve subgroups based on substrate selectivity filter analysis. Expression analyses were performed for a selected set of GmMIPs using semi-quantitative reverse transcription (semi-RT-qPCR) and qPCR. Our results suggested that many GmMIPs have high sequence similarity but diverse roles as evidenced by analysis of sequences and their expression. It can be speculated that GmMIPs contains true aquaporins, glyceroporins, aquaglyceroporins and mixed transport facilitators.

Effect of high temperature on the reproductive development of chickpea genotypes under controlled environments

High temperature during the reproductive stage in chickpea (Cicer arietinum L.) is a major cause of yield loss. The objective of this research was to determine whether that variation can be explained by differences in anther and pollen development under heat stress: the effect of high temperature during the pre- and post-anthesis periods on pollen viability, pollen germination in a medium, pollen germination on the stigma, pollen tube growth and pod set in a heat-tolerant (ICCV 92944) and a heat-sensitive (ICC 5912) genotype was studied. The plants were evaluated under heat stress and non-heat stress conditions in controlled environments. High temperature stress (29/16°C to 40/25°C) was gradually applied at flowering to study pollen viability and stigma receptivity including flower production, pod set and seed number. This was compared with a non-stress treatment (27/16°C). The high temperatures reduced pod set by reducing pollen viability and pollen production per flower. The ICCV 92944 pollen was viable at 35/20°C (41% fertile) and at 40/25°C (13% fertile), whereas ICC 5912 pollen was completely sterile at 35/20°C with no in vitro germination and no germination on the stigma. However, the stigma of ICC 5912 remained receptive at 35/20°C and non-stressed pollen (27/16°C) germinated on it during reciprocal crossing. These data indicate that pollen grains were more sensitive to high temperature than the stigma in chickpea. High temperature also reduced pollen production per flower, % pollen germination, pod set and seed number.

Physiological factors associated with genotype by environment interaction in wheat

Abstract Wheat cultivars often show highly significant genotype by environment interaction (G×E) for yield, even when comparing different years within a relatively stable location. This study attempts to explain some of the physiological bases of G×E in two experiments: (i) historic yield potential trials (HYPTs) of bread wheat ( Triticum aestivum L.), durum ( T. durum Desf.) and triticale (X Triticosecale Wittmack) cultivars grown under agronomically optimal conditions; (ii) an elite spring wheat yield trial (ESWYT) of 30 bread wheat genotypes cultivated at 27 international locations. For the HYPT, the main objectives were to determine the environmental variables during different phenological stages associated with: (i) G×E among the three crop species, (ii) G×E within each species, and (iii) underlying physiological causes of G×E. For ESWYT, meteorological data were not available and so mean site values of certain crop parameters were used as proxy environmental data to determine whether conditions either pre- or post-anthesis were more influential in determining G×E. Partial least-squares analysis and factorial regression models were used to identify the environmental factors best explaining G×E independent of the main effects. Of the three crops, durums were shown to be the most sensitive to conditions pre-anthesis, requiring higher radiation and cooler average temperatures in order to set high grain number. Triticale, despite having the highest average yield and biomass, performed relatively poor when conditions from spike growth stage onwards were sunny and warm. Bread wheat appeared to be the most robust of the three species. Considering yield, biomass, and yield components, it was apparent that the spike primordia growth stage was generally the most sensitive to environmental factors causing G×E. Results for the ESWYT suggested that conditions post-anthesis were more influential on G×E than conditions pre-anthesis. Implications for how such analysis may assist with both conventional and molecular approaches to breeding are discussed.

High yield potential, shuttle breeding, genetic diversity, and a new international wheat improvement strategy

The main elements of the international wheat improvement program of the Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), also known as the International Maize and Wheat Improvement Center, have been shuttle breeding at two contrasting locations in Mexico, wide adaptation, durable rust and Septoria resistances, international multisite testing, and the appropriate use of genetic variation to enhance yield gains of subsequently produced lines. Such an approach yielded successes known collectively as the Green Revolution. However, at the beginning of the 21st century, this “cultivar assembly line” approach needs fine tuning to address crop needs under increasingly adopted resource conserving practices, as well as those related to nutritional requirements of the end-users. International wheat improvement will therefore focus on the targeting of traits in respective mega-environments, and the use of participatory methods, especially in marginal environments. The main features of this wheat improvement strategy include the introduction of new and novel sources of genetic variation through wild species, landraces, and, potentially, the use of transgenes for intractable traits. This variation will be combined using international shuttle breeding, and increased breeding efficiency will be achieved through marker-aided methods, more targeted use of crop physiology, plant genetics, biostatistics, and bioinformatics. Likewise, CIMMYT will increase its focus on the needs of end-users by emphasizing regional efforts in participatory research and client-oriented plant breeding.