Interspecific and intergeneric hybridization as a source of variation for wheat grain quality improvement

Key message

The hybridization events with wild relatives and old varieties are an alternative source for enlarging the wheat quality variability. This review describes these process and their effects on the technological and nutritional quality.

Abstract

Wheat quality and its end-uses are mainly based on variation in three traits: grain hardness, gluten quality and starch. In recent times, the importance of nutritional quality and health-related aspects has increased the range of these traits with the inclusion of other grain components such as vitamins, fibre and micronutrients. One option to enlarge the genetic variability in wheat for all these components has been the use of wild relatives, together with underutilised or neglected wheat varieties or species. In the current review, we summarise the role of each grain component in relation to grain quality, their variation in modern wheat and the alternative sources in which wheat breeders have found novel variation.

     

Genetic variability of Brazilian Indian landraces of Arachis hypogaea L

The Kayabi Indians who inhabit the Xingu Indigenous Park, located in West Central Brazil, have grown and managed peanuts for a long time. A great number of landraces are being maintained by these tribes and some of this germplasm has morphological traits that exceed the variation described in the taxonomic literature. Here, we analyzed the genetic variability of these landraces using a set of microsatellite markers. The analysis showed that, in general, the indigenous samples grouped according to the villages where they were collected. The microsatellite markers used in the present study detected high levels of genetic variation. Similarity groups, genetically distant from each other, were formed, allowing a more efficient use of the existing genetic variability. The present study also showed that these materials can extend the genetic variability available for peanut-breeding programs. Additionally, the microsatellite markers revealed a large dissimilarity among germplasm accessions representing Arachis hypogaea varieties so far included in the same subspecies fastigiata (aequatoriana + peruviana vs fastigiata + vulgaris), a subject that deserves further investigation. Finally, the Xingu Indigenous Park proved to be an important center of diversity for peanut.     

Variability in mammalian dentitions: size-related bias in the coefficient of variation

The coefficient of variation has been used in many evolutionary studies. However, a strong negative correlation between this index and size may artificially inflate the apparent variability of small traits. This is most pronounced when variables whose size differs by more than an order of magnitude are compared or when the index is applied to variables whose size is within an order of magnitude of their measurement error. When this is likely to affect conclusions, other indexes of variability should be considered. One alternative is to use the standard deviation of log-transformed data; however, this index is sometimes still correlated with variable size so care should be exercised in its use. Another alternative is to regress the standard deviation onto mean variable size; however, this method may also be misleading if variables are not randomly distributed about the regression line. As an example of the effect of bias in the coefficient of variation, previous studies of mammalian dental variability profiles were re-evaluated. It was found that variation among teeth is relatively homogenous, both within and among species. The exception is that the canines of some mammalian species have variability that is considerably higher than would be expected from tooth size. Previous explanations of variability patterns that invoked developmental fields are incompatible with the new data.     

The diversification of Citrus clementina Hort. ex Tan., a vegetatively propagated crop species.

Clementines, due to their high quality, are one of the most important cultivated citrus mandarins. As in the case of sweet orange and satsuma mandarins, genetic variability within this species is minimal when analyzed by molecular markers, because the existing varieties have not been obtained through hybridization, but through the selection of spontaneous mutations affecting traits of agronomic interest. This would explain, at least in part, the greater diversity for agronomic traits when compared to the variability for molecular markers. Another possible (nonexclusive) reason is that the types of molecular marker used are not focused on the kind of molecular change mainly involved in the origination of new clementine cultivars; i.e., are all sources of variation equally involved in the diversification of these plants? To answer this question, different kinds of markers based on primers of random sequence, simple sequence repeats, and retrotransposon sequences that may reveal point mutations, and somatic recombination and transposon activity, respectively, were used to compare the level of variability among 24 clementine varieties. Their ISSR, RAPD, and AFLP analysis provided only two polymorphic bands, distinguishing just two varieties. No variability was found by SSRs, i.e., no new allele arising through somatic recombination was detected. Instead, the amplification of sequences adjacent to retrotransposons yielded a higher number of polymorphisms (14.6 vs 2.4% for the previous mentioned marker types). Two geographical distant groups, one from North Africa and the other from Spain, have evolved in agreement with polymorphisms based on IRAP markers anchored to, at least, two different Copia-like retrotransposon sequences. Therefore, this study suggests that the DNA of this type of mobile elements is evolving faster than the DNA of other markers in this clonal lineage.     

Organ-specific and ploidy-dependent somaclonal variation; a new tool in breeding

The organ-specific somaclonal variation means the differences between the variability of somaclones originated from different somatic tissue of plant. Significant differences in some agronomical characters were achieved among somaclones of seed and plumule meristem origin. The ploidy-dependent somaclonal variation means the differences between the variability of somaclones originated from different ploidy-level tissue. Increased variation among regenerated plants was postulated by origin from cultured cells of reduced ploidy level. The comparison of somaclonal variation in the progenies of diploid plants regenerated from callus of haploid and diploid origin supported the ploidy dependent theory. The pollenhaploid somaclone method (PHS-method) was developed and tested for utilization somaclonal variation in rice breeding. The PHS-method comprises the two well-known and widely applied in vitro methods which are the androgenesis (another culture) and genetic instability of cultured haploid somatic cells (callus cultures). Developmental varieties produced by this breeding sheme are under certification in Hungary.     

Variation inLimnanthes alba: A biosystematic survey of germ plasm resources1

Sixteen populations ofLimnanthes alba Bent ham are described for variation in plant growth, floral morphology, and reproductive traits in terms of a biosystematic survey of inter population differentiation. Earlier discussions of two varieties by other botanists are reviewed in relation to our findings of several overlapping and polymorphic population clusters (“races”). Afield evaluation of seed yield at Davis suggested that variability inL. alba be fully described for its use in crop improvement by hybridization and selection.     

Varietal differences in shoot and rooting parameters of pearl millet on sandy soils in Niger

Root parameters are important traits for the acquisition of nutrients and water under resource-limited conditions. In order to investigate the extent of varietal differences in rooting parameters in pearl millet, we compared a total of eight pearl millet varieties in two experiments (ridging and traditional sowing) over four years at the ICRISAT Sahelian Centre, Niger. We found substantial genotypic variation for root length density (RLD), root dry matter, and total root length (RL), but not for specific root length, depth of rooting, or partitioning of roots between topsoil and subsoil (>20 cm depth). RL showed a highly dynamic pattern over the growing season. RL and shoot dry matter were positively correlated over P supplies and contrasting levels of field productivity. The relationship between RL and grain yield as well as harvest index were less clear. The root fraction responded to variation in soil productivity, increasing from roughly 20% under high productivity to more than 40% at low productivity, but we found no evidence of varietal differences in this trait despite pronounced differences in maturity and plant stature. Identification of pearl millet varieties suited for growth under low input conditions in south-west Niger can potentially make use of existing genotypic variability in root parameters, but we suggest that, due to high variability for root traits, indirect selection for shoot parameters (e.g., number of stems) is more promising than direct selection for RLD or RL.     

Effect of inversion polymorphism on the neutral nucleotide variability of linked chromosomal regions in Drosophila

Recombination is a main factor determining nucleotide variability in different regions of the genome. Chromosomal inversions, which are ubiquitous in the genus Drosophila, are known to reduce and redistribute recombination, and thus their specific effect on nucleotide variation may be of major importance as an explanatory factor for levels of DNA variation. Here, we use the coalescent approach to study this effect. First, we develop analytical expressions to predict nucleotide variability in old inversion polymorphisms that have reached mutation-drift-flux equilibrium. The effects on nucleotide variability of a new arrangement appearing in the population and reaching a stable polymorphism are then studied by computer simulation. We show that inversions modulate nucleotide variability in a complex way. The establishment of an inversion polymorphism involves a partial selective sweep that eliminates part of the variability in the population. This is followed by a slow convergence to the equilibrium values. During this convergence, regions close to the breakpoints exhibit much lower variability than central regions. However, at equilibrium, regions close to the breakpoints have higher levels of variability and differentiation between arrangements than regions in the middle of the inverted segment. The implications of these findings for overall variability levels during the evolution of Drosophila species are discussed.     

So Many Brands and Varieties to Choose from: Does This Compromise the Control of Food Intake in Humans?

The recent rise in obesity is widely attributed to changes in the dietary environment (e.g., increased availability of energy-dense foods and larger portion sizes). However, a critical feature of our “obesogenic environment” may have been overlooked - the dramatic increase in “dietary variability” (the tendency for specific mass-produced foods to be available in numerous varieties that differ in energy content). In this study we tested the hypothesis that dietary variability compromises the control of food intake in humans. Specifically, we examined the effects of dietary variability in pepperoni pizza on two key outcome variables; i) compensation for calories in pepperoni pizza and ii) expectations about the satiating properties of pepperoni pizza (expected satiation). We reasoned that dietary variability might generate uncertainty about the postingestive effects of a food. An internet-based questionnaire was completed by 199 adults. This revealed substantial variation in exposure to different varieties of pepperoni pizza. In a follow-up study (n= 66; 65% female), high pizza variability was associated with i) poorer compensation for calories in pepperoni pizza and ii) lower expected satiation for pepperoni pizza. Furthermore, the effect of uncertainty on caloric compensation was moderated by individual differences in decision making (loss aversion). For the first time, these findings highlight a process by which dietary variability may compromise food-intake control in humans. This is important because it exposes a new feature of Western diets (processed foods in particular) that might contribute to overeating and obesity.     

Use of molecular markers in participatory plant breeding: assessing the genetic variability in cotton populations bred by farmers

In participatory plant breeding, farmers are involved in simple selection schemes that are not suitable for assessing genetic variability in the segregating populations. We propose to use information derived from molecular marker analyses to help monitoring such populations. In this study, we used three indicators to compare genetic variability in eight genetic structures, that is three plant populations selected by farmers over five generations, three nonselected populations and two commercial varieties. The three indicators were the polymorphic locus rate, heterozygosity rate and dissimilarity index. The results highlighted that the genetic variability decreased more with farmers’ selection than with environmental factors. The breeding process was not complete because genetic variability in the selected populations was midway between that of the nonselected populations and that of the commercial varieties monitored. The three proposed indicators were relevant for describing the studied populations. They could be interpreted according to a grid drawn up on the basis of the results of the present study.     

Isozyme characterization of dikaryotic strains of the edible basidiomyceteAgaricus bitorquis (Quel.) Sacc. (syn.Agaricus edulis)

Seven isozyme activities were studied by isoelectric focusing and blotting of total protein extracts of dikaryotic strains ofAgaricus bitorquis (Quel.) Sacc. (syn.Agaricus edulis) to characterize strains and varieties and to provide information for subsequent protection of new putative commercial varieties. Isoelectric focusing gave reproducible patterns and blotting onto nitrocellulose membrane increased the sensitivity of enzyme detection. Five activities showed high variability: alcohol dehydrogenases, dopa-reacting enzyme phenoloxidases, tolidine-reacting enzyme phenoloxidases, esterases, and peroxidases. Two activities, diaphorases and acid phosphatases, presented low variability. Compilation of patterns obtained for the seven isozyme activities allowed the distribution of the closely genetically related varieties into separate groups. The five enzyme activities with high variability were sufficient to discriminate all theA. bitorquis varieties tested and to define a method for characterization and protection of new strains. Analysis of these patterns and comparison with other higher fungi showed that the variability inA. bitorquis is comparable with those described forPleurotus eryngii, Coprinus congregatus, and·Lentinus edodes, and higher than the variability found forAgaricus bisporus.     

Genetic diversity analysis of isolates of the fungal bean pathogen Pseudocercospora griseola from central and southern Brazil

Planting resistant varieties is the most effective control measure against the angular leaf spot of dry beans, a fungal disease caused by Pseudocercospora griseola. However, dry bean varieties with durable resistance are not easily obtained. Knowledge about the genetic variability of the pathogen population is key for the success of dry bean breeding programs aimed at developing resistant materials, but finding suitable operationally simple and genetically accurate markers is not an easy task. The aim of this study was to assess the suitability of the ISSR-PCR technique to quantify the genetic variability of P. griseola isolates. Total DNA of 27 P. griseola isolates from Goiás, Minas Gerais, Espírito Santo, and Paraná States was extracted and amplified using specific primers for ISSR. Using cluster analysis, 27 genotypes were identified. The ISSR-PCR technique was suitable for assessing intraspecific variability of P. griseola. The ISSR-PCR marker was found to be highly sensitive to genetic variation and can aid in elucidating the genetic structure of the population of this plant pathogen as a support tool for the dry bean breeding programs.     

Study of the intra-cultivar variability of grape DNA using RFLP and PCR methods

Evaluation of DNA polymorphism among Vitis vinifera varieties using RFLP and PCR methods has been performed to choose a DNA technology for detection of grape intracultivar variation. DNA polymorphism of clones of the varieties Riparia Gluar, Riparia x Rupestris 101-14, Cabernet Sauvignon, Riestling reinskiy has been studied using Southern hybridization and amplification techniques. It has been shown that grape intracultivar variability of rDNA in Riparia x Rupestris 101-14 and Cabernet Sauvignon clones was caused by the modification in Alul restriction sites of rDNA. DNA variability of the randomly amplified and inter-SSR sequences of the Riparia Gluar, Riparia x Rupestris 101-14, Cabernet Sauvignon clones was also detected. A set of molecular DNA loci which can be used for grape clone identification has been obtained.     

Assessment of Genetic Diversity in <Emphasis Type="Italic">Trigonella foenum-graecum</Emphasis> Based on Nuclear Ribosomal DNA,Internal Transcribed Spacer and RAPD Analysis

Fenugreek (Trigonella foenum-graecum) is receiving global attention due to rare medicinal properties of significance to human health. Gene banks possess scanty germplasm and very little background information regarding its genetic variability that has hampered its improvement. We investigated the extent of variability among 17 Indian varieties of fenugreek using phenotypic and genetic markers. Multilocus genotyping by ten random amplified polymorphic DNA (RAPD) primers detected an average of intraspecific variations amounting to 64.7% polymorphism in banding patterns. Analysis of molecular variance indicated that a greater proportion of total genetic variation exists within population (91%) rather than among populations. Higher values of Nei’s gene diversity (h) and Shannon Information Index (i) and genetic distance analysis validate higher genetic diversity among Indian fenugreek varieties. SNPs at 14 sites of rDNA region revealed further lineages of distinct varieties with main RAPD clusters. The representative sequences of each subgroup and all distinct varieties have been submitted to NCBI database and assigned Gen Accession numbers HM 176640–176649. The measures of relative genetic distances among varieties of fenugreek did not completely correlate with the geographical distances of places of their development. The homogeneous phenotypic markers proved insufficient in exhibiting genetic divergence among fenugreek varieties studied. Eventually, the knowledge of their genetic relationships, DNA bar coding and phylogenies might contribute for the designing of intraspecific crosses between cultivars of this fenugreek collection with potential interest in seed spices breeding programme.     

Studies on some genetic parameters of rice (Oryza sativa L.)

Summary In order to utilize the available useful variation in breeding rice to improve yield and quality of grain, the performance of a wide range of rice germ plasm comprising 30 varieties was evaluated in northern India, a major rice growing belt. Plant performance revealed high genetic divergence and phenotypic variability in the crop, with the maximum range of variation being for grain number per panicle and the minimum for grain dimensions. There were also significant differences among varietal means for ten phenotypic traits. Genotypic and phenotypic variance contributed profoundly to the variance of the phenotypic traits studied, but, since genetic variability in the traits related to yield was considerable, there is scope for further improvement in yielding ability. Grain number per panicle, number of effective tillers per plant and culm length exhibit high heritability, and genotypic coefficient of variation and therefore a high genetic advance. Thus, selection for these traits would be effective in crop improvement. Moreover, grain number per panicle shows a significant positive correlation with yield, and this trait could profitably form a reliable index for the yielding capacity of this crop.     

Linkage disequilibrium in synthetic varieties of perennial ryegrass

Synthetic varieties obtained after three to four panmictic generations are variable, not structured and so can be used for association studies. The pattern of linkage disequilibrium (LD) decay determines whether a genome scan or a candidate gene approach can be used for an association study between genotype and phenotype. Our goal was to evaluate the effect of the number of parents used to build the synthetic varieties on the pattern of LD decay. LD was investigated in the gibberelic acid insensitive gene (GAI) region in three synthetic varieties of perennial ryegrass (Lolium perenne L.) chosen for their contrasted number of parents in the initial polycrosses. Results were compared with those obtained from a core collection. STS and SSR markers were used to evaluate variation, structuration and LD in each variety. As expected, the varieties variability increased with the number of parents almost up to the core collection variability. No structuration was observed in the varieties. Significant LDs were observed up to 1.6 Mb in a variety originated from six related parents and not above 174 kb in a variety originated from 336 parents. These results suggest that a candidate gene approach can be used when varieties have a large number of parents and a genome scan approach can be envisaged in specific regions when varieties have a low number of parents. Nevertheless, we strongly recommend to estimate the pattern of LD decay in the population and in the genomic region studied before performing an association study.     

Genetic characterization of Bhutanese native chickens based on an analysis of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), domestic Southeast Asian and commercial chicken lines (Gallus gallus domesticus)

The genetic diversity of Bhutanese chickens needs to be understood in order to develop a suitable conservation strategy for these birds in Bhutan. In this, work, we used microsatellite markers to examine the genetic diversity of Bhutanese chickens. Four Bhutanese chicken varieties (Black plumage, Frizzle, Naked neck and Red Junglefowl-like, corresponding to Yuebjha Narp, Phulom, Khuilay and Seim, respectively), two subspecies of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), two varieties of Thai native chickens (Pradhu Hang Dam and Chee; Gallus gallus domesticus) representing the Southeast Asian domestic chicken, and two commercial lines (Broiler and Single Comb White Leghorn) were genotyped with 18 microsatellites that included 16 loci recommended by the FAO/ISAG for investigations of genetic variability in chickens. All loci were polymorphic, with the number of alleles ranging from six (MCW0111) to 23 (MCW0183). Substantial genetic variation was observed in all populations, with the Bhutanese native chicken Yuebjha Narp (Black plumage chicken) showing the lowest genetic variability. Despite extensive intrapopulation variation, the genetic differentiation among 10 populations was moderate. A neighbor-joining tree revealed the genetic relationships involved while principal component analysis showed that Bhutanese native chickens should be given priority in conservation efforts because of their genetic distinctiveness. Chee chickens are especially valuable as a reservoir of predomestic diversity, as indicated by their greater genetic variation and their position in the phylogenetic tree.     

VARIATION WITHIN FRENCH BEAN VARIETIES

The internal variability of several varieties and strains of French bean is investigated, confining attention to the single character, seed weight. Out of eleven strains examined only two appeared to be homogeneous for seed weight, whilst two were obviously heterogeneous even by superficial examination of the seed.
A comparison of the distribution of seed weights in five strains of Canadian Wonder showed that each strain contains at least two or three lines out of the minimal estimate of four shared between them.
The natural out-crossing of fourteen varieties, including those analysed for seed weight, is compared. There are indications that varieties vary in their out-crossing propensities. No indication was found of the causes of the high frequencies of out-crossing occasionally encountered.
The possible sources of intra-varietal variation are briefly surveyed.     

Characterization of the (GAAA) microsatellite region in the plant parasitic nematode Meloidogyne artiellia

Microsatellites have become one of the most powerful genetic markers in biology. We have used DNA sequencing to characterize a highly variable microsatellite (GAAA) locus in the root-knot nematode Meloidogyne artiellia. The use of microsatellite flanking primers produced four amplification products that are defined as electromorphs, based on conventional length criteria. The sequencing of these four amplification products revealed the presence of new variants in the population due to sequence variability. The sum of electromorphs and sequence polymorphisms resulted in a total of six variants. The high degree of variability in the microsatellite containing region is due not only to variation in the number of tetranucleotide repeats but also to variation (length and site variation) in the flanking regions of the microsatellite. These investigations show that, in spite of the size homoplasy, the variability of the microsatellite flanking sequences of M. artiellia could be used as informative markers for phylogenetic reconstructions.