Genetic diversity of wheat storage proteins and bread wheat quality

To understand the genetic and biochemical basis of the bread makingquality of wheat varieties, a large experiment was carried out with a set of162 hexaploid bread wheat varieties registered in the French or EuropeanWheat Catalogue. This material was used to analyse their allelic compositionat the twelve main storage protein loci. A large genetic and biochemicaldiversity of the gluten proteins was found. Several gliadin encoding lociexhibited the highest allelic diversity whereas the lowest diversity was foundfor Glu-A1 and Glu-D3 loci encoding some high molecularweight glutenin subunits (HMW-GS) and LMW-GS respectively. Thevarieties were grown in three experimental locations in France. Qualityevaluation was carried out from material harvested in each location usingseven technological tests: grain protein content (Prot), grain hardness(GH), Zeleny sedimentation test (Zel), Pelshenke test (Pel), water solublepentosans (relative viscosity: Vr ), mixograph test (giving 11 parameters)and the alveograph test (dough strength W, tenacity P , extensibility L,swelling G, ratio P/L and the elasticity index Ie). Genetic and locationeffects as well as broad-sense heritability of each of the 22 technologicalparameters were calculated. GH, corresponding to the major Ha gene, Pel,and MtxW (mixograph parameter) had the highest heritability coefficients,alveograph parameters like W, P, the relative viscosity Vr and severalmixograph parameters had medium heritability coefficients whereas Protand L had the lowest. Variance analysis (using GLM procedure) allowed theeffect of the allelic diversity of the storage proteins, on the geneticvariations of each quality parameters, to be estimated. Glu-1 and Glu-3 loci had significant additive effects in the genetic variations of manyparameters. Gliadin alleles encoded at Gli-1 and Gli-2 were alsofound to play significant effect on several quality parameters. The majorpart of the phenotypic variation of the different quality parameters like Zel,Pel, W or mixograph peak time MPT was explained with the GH and allelesencoded at Glu-1 and Glu-3. Allelic variants encoded at Glu3and Gli-2 had similar contribution to the phenotypic variations ofquality parameters and accounted for 4% up to 21% each.     

Patterns of RFLP-based genetic diversity in germplasm pools of common wheat with different geographical or breeding program origins

A set of 292 accessions of common wheat (Triticum aestivum L.) representing 21 germplasm pools based on geographical or breeding program origins was assayed for RFLP diversity. Thirty cDNA and genomic DNA probes and the HindIII restriction enzyme were employed for RFLP analysis. About 61% of all 233 scored bands were present in 75% or more of the accessions. All but one of the 30 probes revealed polymorphism, and the average number of distinct patterns per probe over all accessions was 9.5.Polymorphic Information Content (PIC) values within a pool varied from 0 to 0.9 and depended on the identities of both the germplasm pool and the probe. Rare banding patterns with a relative frequency of ≤0.2 within a pool were detected. These rare patterns were more likely to occur in pools exhibiting high levels of heterogeneity. The highest level of polymorphism was observed in the Turkish landraces from Southwest Asia. The Eastern U.S. soft red winter wheat germplasm pool was more genetically diverse than the other advanced germplasm pools, and nearly as diverse as the Turkish landrace pool. RFLP-based genetic relationships between germplasm pools generally tracked expectations based on common geographical origin, breeding history and/or shared parentages. The Chinese wheat landraces from Sichuan, Tibet, and Yunnan provinces were distinct from other pools. Similarity matrices for among-pool genetic distance estimates based on either band frequencies or banding pattern frequencies showed good correlation with matrices derived from Nei and Li's mean genetic similarity estimates (r=−0.82^** and r=−0.73^**, respectively. This revised version was published online in July 2006 with corrections to the Cover Date.     

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

Summary The dangers of a narrow genetic base of the world's 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 Roger's 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.     

Impact of plant genetic resources on wheat breeding

This article describes the impact of plant genetic resources on wheat breeding. It defines the important contribution of N.I. Vavilov Institute (St. Petersburg, Russia) to broadening the genetic diversity of new wheat cultivars. Special attention is given to conducting a comprehensive evaluation of intraspecific variability for valuable characters, including: 1) formation of special subcollections, consisting of accessions with useful characters and accessions representing intraspecies diversity for a given character; 2) revealing genetic differences among phenotypically superior accessions; 3) determining a genetic system of intraspecific variability for a given character; 4) formation of a genetic collection; 5) revealing and developing the donors of useful characters. An example using plant height shows that the proposed research approach adequately determines the genetic potential of species and reveals the most effective genes for practical uses. It is assumed that the main sources of genes for breeding Triticum aestivum L. in order of importance will remain: 1) intraspecific diversity of T. aestivum itself; 2) other Triticum species; 3) other genera of the Triticeae Dum. tribe (particularly Aegilops L.); 4) more remote genera of the Poaceae Barnh. botanical family. It is stressed that existing diversity of T. aestivum has been poorly investigated genetically and only partially used by breeders. Properly evaluated, it can provide multiple solutions for traditional and new problems of wheat improvement. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic diversity of high-molecular-weight glutenin subunit compositions in landraces of hexaploid wheat from Japan

The high-molecular-weight (HMW) glutenin subunit composition of seed storage protein of 174 Japanese hexaploid wheat (Triticum aestivum) landraces have been examined by using sodium dodecyl sulfate polyacrylamide gel electrophoresis system. Twenty four different, major glutenin HMW subunits were identified, and each of the landraces contained three to five subunits and 17 different glutenin subunit patterns were observed for 13 alleles in the landraces. On the basis of HMW glutenin subunits composition, Japanese landraces showed a specific allelic variation, close to Japanese commercial wheats in HMW glutenin subunits, different from those in alien hexaploid wheats. Further, it could be concluded that all common glutenin alleles can be found in the 174 landraces originated from Japan. The variation detected in the glutenin subunits is useful for variety identification, has a bearing on our understanding of hexaploid wheat genetic resource evolution in Japan, and raises questions concerning the nature of this genetic variation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity in bread wheat, as revealed by coefficient of parentage and molecular markers, and its relationship to hybrid performance

Variable results have been obtained in different crop species using geneticsimilarity (GS) estimates based on molecular markers and coefficient ofparentage (COP) to predict heterosis.This study was designed: i) to assess the level of GS among 40 breadwheat (Triticum aestivum L.) cultivars selected in Central and SouthEurope; ii) to compare GS with COP; iii) to correlate the estimates ofparental diversity with the heterotic effects detected on 149 F₁hybrids obtained by crossing the 40 cultivars according to three matingdesigns.The parental cultivars and the F₁ hybrids were grown in severallocations at normal seed density. Significant heterotic effects were detectedfor grain yield and other traits including quality attributes. The parentalcultivars were assayed for DNA polymorphisms using two classes ofmarkers: 338 RFLP and 200 AFLP^® bands were scored. GS estimates werecomputed considering each molecular marker set separately (GS_RFLP,GS_AFLP) and together (GS_TOT). Ample differentiation amongthe parental cultivars was detected with the two marker sets. Although theaverage GS_TOT (0.43) was higher than COP (0.10), the twomeasurements were significantly correlated (r = 0.36, p < 0.01).Correlations between the different estimates of genetic diversity andF₁ performance or mid parent heterosis for grain yield and otherrelated traits were in general low although statistically significant.A more detailed analysis was conducted on 28 F₁ hybridsproduced in a half diallel cross of eight parental cultivars characterized byhigh heterotic effects for grain yield. The GS estimates based on RFLP,AFLP^® markers and also on RAPD were partitioned into general andspecific components. Correlations with general and specific combiningability effects for the measured traits were in several cases statisticallysignificant but too low to be predictive and therefore exploitable in practicalbreeding.     

Assessment of the spatial genotypic and phenotypic diversity present in the various winter wheat breeding programs in Southeast Europe

The genetic diversity present in the breeding programs of southeast Europe was assessed in a set of 114 winter wheat (Triticum aestivum L.) cultivars using AFLP and SSR markers. The average genetic diversity characterised with the Jaccard’s distance coefficient was 0.605 with an interval of 0.053 and 0.889. The wheat cultivars originating from the four countries differed from each other in their clustering patterns, including the numbers of clusters and the most prevalent cluster, which was breeding program-specific. Hungarian and Romanian cultivars showed closer relationships, and Serbian and Macedonian cultivars grouped together more frequently. The phenotypic variability of the same cultivars was assessed under diverse ecological conditions of the four growing sites, measuring the disease resistance against two foliar diseases, and several agronomic traits. Of the phenotypic traits, powdery mildew and leaf rust responses showed significant associations with genetic diversity, whereas heading date, plant height and yield components did not. Through parallel assessment of genotypic and phenotypic diversity it was possible to separate winter wheat cultivars with similar genotype but diverse phenotype from those with similar phenotype but diverse genotype. This information will allow breeders to make informed decisions in selecting parents for new crosses.     

Recurrent selection using male sterility and hydroponic tiller culture in pedigree breeding of wheat

A procedure for recurrent selection based on the male sterility gene, Ms3, was implemented. To facilitate the production of large numbers of hybrid progeny, a simple hydroponic system was developed in which male‐sterile tillers cut at the flowering stage can be pollinated and maintained for about 8 weeks‐long enough to produce a large quantity of viable hybrid seeds. The recurrent selection steps were integrated with a pedigree breeding programme employing different selection cycles for male and female plants. F₁ female plants are subjected to a single screening for seedling resistance. In addition to F₁ seedling screening, F₂‐F₄ male families are field‐selected for disease resistance, agrotype and quality in a pedigree programme before being used in crosses.     

Applications of pedigree-based genome mapping in wheat and barley breeding programs

The aim of the pedigree-based genome mapping project is to investigate and develop systems for implementing marker assisted selection to improve the efficiency of selection and increase the rate of genetic gain in breeding programs. Pedigree-based whole genome marker application provides a vehicle for incorporating marker technologies into applied breeding programs by bridging the gap between marker–trait association and marker implementation. We report on the development of protocols for implementation of pedigree-based whole genome marker analysis in breeding programs within the Australian northern winter cereals region. Examples of applications from the Queensland DPI&F wheat and barley breeding programs are provided, commenting on the use of microsatellites and other types of molecular markers for routine genomic analysis, the integration of genotypic, phenotypic and pedigree information for targeted wheat and barley lines, the genomic impacts of strong selection pressure in case study pedigrees, and directions for future pedigree-based marker development and analysis.     

Morphological and molecular characterization of Italian emmer wheat accessions

Summary The characterization of 39 Italian ecotypes and cultivars of Triticum turgidum L. spp. dicoccum Shrank ex Schübler (emmer wheat) was performed utilizing agro-morphological and molecular tools. Emmer wheat is a hulled species which grows wild in the Near East and is still cultivated in the Mediterranean Basin. Due to its characteristics, in Italy it is cultivated mainly in marginal lands of central and southern Italy, where local varieties, adapted to the natural environment where they originated, are used. Emmer wheat cultivation has been drastically reduced during the last century as a consequence of its low yield. Nevertheless, more recently, its agronomic and nutritive values, together with its use in health food products, made its cultivation economically viable in the marginal lands with a parallel increase of the cultivated area which is now more than 2000 ha. In the present paper the results of morphological evaluation, carried out in an experimental field in central Italy using a randomized block design with three replications, and molecular characterization are reported. The analysed material showed distinctive molecular traits and the existence of a huge amount of diversity not only between varieties, but also within them. When the accessions were clustered utilizing their genetic distance, the clusters were not always in agreement with the accessions origins. The obtained results gave information that can be useful for: (i) future registration of material, (ii) germplasm conservation and (iii) use of this valuable source of emmer germplasm for future breeding programmes.     

Discriminating maize inbred lines using molecular and DUS data

Growing numbers of candidate varieties, decrease of their variability for morphological traits, and internationalization of the national list all contribute to excessive increase of the trial costs, thus creating the need for the improvement of current variety evaluation procedures, especially regards their distinctness, Uniformity, and Stability (DUS) component. Due to rapid advancement in molecular techniques, the use of molecular markers in DUS testing as a complement to, or replacement of, morphological observations became the subject of great interest in scientific studies, and consequently topic for discussion within International Union for the Protection of New Varieties of Plants (UPOV). In order to explore the potential of simple sequence repeat (SSR) markers for distinctness tests, present study involved set of 41 maize inbred lines that were scored for 32 DUS characters prescribed by UPOV and genotyped at 28 SSR loci. Results were largely in favor of the use of molecular markers, revealing or confirming their already known advantages over morphological markers like better consistency with the pedigree, and relatively higher discriminative power. However, their integration into DUS testing protocols still depends upon resolving of several important issues.     

Genetic diversity inHippophae L. and its use in plant breeding

Summary In the last decade,Hippophae species, particularlyH. rhamnoides L., has received special attention in several countries for its multiple uses. The plant produces edible fruit with high nutrient and medicinal values and is characterized by its nitrogen-fixing symbiosis. It is widely distributed on the Eurasian continent (27°–69° N). Wide genetic variation is the basis of its distribution and provides good opportunities for selection and breeding.Hippophae is extremely variable in height, from a small bush less than 50 cm to a tree more than 20 m high. Phenological observations have shown a clear gradient of growth rhythm and plant size corresponding to the geographical distribution from north to south inH. rhamnoides. Studies on vitamin C concentration in the fruit have revealed significant differences between and within natural populations. The fruit size varies from 4 to 60 g/100 berries, the fruit color, from yellow, orange to red, and the shape, from flat, round, oval to cylindrical. Isozyme studies have shown that the mean number of alleles per locus per population is 2.1 and the percentage of polymorphic loci was 40.3% (at 0.95 standard). There is large genetic diversity residing within and between subspecies and species in the genusHippophae.     

Genetic relatedness among eastern North American blackberry cultivars based on pedigree analysis

Blackberry genetic relationships (Rubus subgenus Rubus Watson) have not been thoroughly studied. The University of Arkansas maintains one of the largest blackberry-breeding programs in the world and thus, in-depth knowledge of the cultivars released from the program and others instrumental in their lineages can aid in breeding endeavors. Pedigrees of 32 cultivars were traced to their founding clones. Genetic contribution (GC), maximum potential similarity (MPS), inbreeding coefficient, and coefficients of relationship (CR) were calculated for all genotypes. Nineteen founding clones contributed to the 32 cultivars, ranging from <1% to 19%. The top three founding clones for mean GC conferred nearly 50% to the 32 cultivars in this study, suggesting a somewhat narrow genetic base. Calculations for MPS ranged from complete similarity (1.00) to 0.00. Individual inbreeding coefficients ranged from 0.00 to 0.25. The coefficient of relationship was used as a method of determining genetic relatedness and ranged from 0.00 to 0.74. University of Arkansas cultivars had the highest MPS and CR in the study. This may be attributed to more generations of hybridization than the other cultivars. The MPS provided some comparable results to those of RFLP and RAPD molecular studies, but CR did not. The rather narrow genetic base of eastern North American blackberry cultivars does not create an imminent, significant concern for loss of diversity. However, more diverse germplasm should be infused for continuation of heterogeneity.     

Assessment of the uniformity of wheat and tomato varieties at DNA microsatellite loci

By analysing a number (20–38) of individuals from selected varieties of wheat and tomato, we have been able to assess intra-varietal uniformity at certain micro satellite (simple sequence repeat, SSR) loci. In total, 45 varieties of wheat were analysed at between 7–9 different SSR loci, and 10 varieties of tomato were analysed at six loci. The results showed that there was variation both between varieties and between microsatellites in the degree of non-uniformity observed, and it was possible to identify a number of different probable sources of non-uniformity. Twenty-four of the wheat varieties and nine of the tomato varieties were sufficiently uniform to meet the standards currently applied for distinctness, uniformity and stability (DUS) testing using phenotypic characteristics. The implications for the potential future use of SSRs in DUS testing are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Homologous analysis of SSR-ESTs and transferability of wheat SSR-EST markers across barley, rice and maize

Summary Comparative genetic analysis has shown that different plant species often share orthologous genes for very similar functions, especially for cereal crops. In this study, we focused on analyzing the utility of EST-SSR markers among monocots in silico and by experiment. Based on 423,611 wheat ESTs, 101,299 were found to express commonly in rice, maize and barley ESTs, which accounted for 23.94% of wheat EST data. 1707 SSR-containing ESTs (SSR-ESTs) were mined from the 101,299 homologous ESTs, which accounted for 8.8% of all the 19,434 wheat EST-SSRs. It showed that the number of homologous SSR-ESTs much less than the homologous ESTs among grasses. The number of conserved ESTs and SSR-ESTs were inversely proportional to the evolutionary distance among species. Although these SSR-ESTs were in high similarity, the number of conserved SSRs between wheat and the other three crops decreased with the increased aligning regions, and only 13 types of SSR motifs in 21 ESTs were obtained by aligning sequences over a stretch of more than 40 bp. The variation at a microsatellite came from not only the differences in the numbers of repeat units and its location shift, but also base mutations flanking microsatellite repeats. From the 428 uni-SSR-ESTs universally in the four cereals, 243 primers were designed and tested in two genotypes of each species. 154 (63.4%) primers produced clear amplicons across the four species, which showed a high efficient transferability of wheat EST-SSR markers to the other three cereal crops.     

Genetic diversity in soybean as determined by RAPD and microsatellite analysis

The random amplified polymorphic DNA (RAPD) and microsatellite techniques were used to evaluate the genetic diversity among 18 soybean genotypes selected for a breeding programme to increase the protein content of varieties adapted for central European growing conditions. Out of 33 random primers used in RAPD reactions, only 12 showed polymorphism useful for characterization of these genotypes. In contrast, all 12 microsatellite primer pairs used in this study detected polymorphism with 2–6 alleles per locus. Similarity measures and cluster analysis were made using RAPD and simple sequence repeat (SSR) data, separately and together. The resulting dendrograms were compared with each other and with the available pedigree information as a control. The dendrogram derived from RAPD data showed some divergence from the pedigree information available for the lines. The dendrograms based on SSR data and SSR data combined with RAPD gave very good agreement with pedigree information. It can be concluded that the combined use of a limited number of RAPD and SSR markers is a useful and reliable means of evaluating genetic relationships of genotypes in the absence of pedigree data.     

Genetic variation for waxy proteins and starch properties in Italian wheat germplasm

Granule-bound starch synthase (GBSS) is the primary enzymeresponsible for the synthesis of amylose in amyloplasts of cereal endospermcells. In bread wheat there are three structural genes (Wx-A1, Wx-B1,and Wx-D1) encoding for isoforms of GBSS. The loss of one or moreGBSS isoforms results in the reduction (partial-waxy) or absence (waxy) of amylose in the starch. Waxy wheats may find application inthe production of modified food starch and their flour may be used toextend the shelf life of baked products. In order to breed high qualitywheats able to produce bread with delayed staling, the genetic variabilityfor the waxy trait in our germplasm has been investigated. Weanalysed 288 cultivars of bread wheat, 139 cultivars of durum wheat andabout 200 accessions from other Triticum species. Gel electrophoresisshowed 63 bread wheats deficient in the Wx-B1, one in the Wx-A1 and one in the Wx-D1 protein isoforms, as well as one Triticum dicoccum lacking the Wx-A1 isoform. None of the analysedTriticum monococcum, Triticum durum, Triticum speltaand Triticum timopheevi accessions showed mutations at the Wxloci. The wheat accessions with Wx mutations were evaluated with aRapid Visco Analyser (RVA) to investigate starch properties. All theanalysed cultivars showed Peak Viscosity and Final Viscosity different fromthe normal wheat. Other analyses to evaluate the rheological characteristicsof the partial-waxy genotypes are under way and a breedingprogramme to select new waxy wheat varieties is in progress     

Genetic diversity of new maize hybrids based on SSR markers as compared with other molecular and biochemical markers

Genetic diversity of four new yellow single crosses, five new yellow three-way crosses, and five yellow inbred lines of maize (Zea mays L.) was studied using different molecular (SSR, ISSR, and RAPD) and biochemical markers (seed storage protein content). All markers were able to clearly separate the inbred lines in one cluster from the different types of hybrids. The correlation among the different types of molecular markers was moderately high according to the Mantel’s test (e.g. 0.67 between SSR and ISSR, 0.42 between SSR and RAPD, and 0.65 between ISSR and RAPD), indicating that the three techniques are efficient for evaluating genetic diversity in the maize genotypes. The correlation of biochemical markers (seed storage protein SDS-PAGE) with SSR, ISSR, and RAPD markers was 0.61, 0.74, and 0.48, respectively. It can be concluded that both molecular and biochemical markers are efficient to study the genetic diversity in maize. Among the different types of molecular markers, SSR is a more accurate marker-type because of its co-dominance and stability of results. It can also be said that biochemical and molecular markers are positively correlated and the correlation ranged between moderate to high. This could suggest using both marker types, separately or together, for genetic diversity studies in maize.     

A comparison between single seed descent and early cross selection in wheat breeding

Summary Two selection procedures in wheat breeding were compared on the basis of their ability to supply high yielding inbred lines. The first procedure consists of an early selection between crosses in the F₃ generation, based on predictions of the cross mean and the between line variance. In the second procedure selection is postponed until the F₆, which is derived by single seed descent. The two procedures are evaluated in a two year test, using pseudo-lines of spring wheat. These pseudo-lines consist of mixtures of varieties and enable an estimation of the exact genetic parameters. In this way the accuracy of the predictions can be examined.In case of early selection, it appears that the predictions of the cross mean and especially the between line variance are very inaccurate. This is caused by the effects of plot size, intergenotypic competition and, to a lesser extent, dominance and/or epistasis. It results in an erroneous ranking of the crosses and the discarding of the potentially best cross. The F₆-SSD line estimates are much more accurate and thus the better lines are indeed selected. A first comparison between the two selection procedures therefore indicates a preference to the SSD method.     

Genetic diversity of barley cultivars grown in Spain, estimated by RFLP, similarity and coancestry coefficients

This study was conducted with the objective of characterizing the genetic variation among a representative set of 37 barley cultivars currently grown in Spain, using restriction fragment length polymorphism (RFLP) markers. Thirty-two RFLP probes, in combination with three restriction enzymes, were used to analyse polymorphism at the molecular level. Genetic distances (GD), based on RFLP band patterns, and coancestry coefficients (f), based on pedigree records, were calculated. Of the 95 clone-enzyme combinations analysed, 71 (74.7%) were polymorphic, representing 246 RFLP patterns. A cluster analysis of GD split the sample into five distinct germplasm groups that were consistent with the history of the cultivars (winter European, spring European, CIMMYT-ICARDA materials, the single cultivar ‘Dobla’ and Spanish local materials). The Spanish group was the most distinct one and had unique alleles at markers close to major loci determining phonological adaptation. The probes which best distinguished among groups were also identified. Genetic similarity estimates were moderately consistent with f (for cultivars with complete pedigrees). The implications for integration of diversity studies into breeding programmes are discussed.