Mireille Khairallah

Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat.

Abstract.In hexaploid bread wheat (Triticum aestivum L. em. Thell), ten members of the IWMMN (International Wheat Microsatellites Mapping Network) collaborated in extending the microsatellite (SSR = simple sequence repeat) genetic map. Among a much larger number of microsatellite primer pairs developed as a part of the WMC (Wheat Microsatellite Consortium), 58 out of 176 primer pairs tested were found to be polymorphic between the parents of the ITMI (International Triticeae Mapping Initiative) mapping population W7984 × Opata 85 (ITMIpop). This population was used earlier for the construction of RFLP (Restriction Fragment Length Polymorphism) maps in bread wheat (ITMImap). Using the ITMIpop and a framework map (having 266 anchor markers) prepared for this purpose, a total of 66 microsatellite loci were mapped, which were distributed on 20 of the 21 chromosomes (no marker on chromosome 6D). These 66 mapped microsatellite (SSR) loci add to the existing 384 microsatellite loci earlier mapped in bread wheat.

A method for combining molecular markers and phenotypic attributes for classifying plant genotypes

Abstract  Classifying genotypes into clusters based on DNA fingerprinting, and/or agronomic attributes, for studying genetic and phenotypic diversity is a common practice. Researchers are interested in knowing the minimum number of fragments (and markers) needed for finding the underlying structural patterns of diversity in a population of interest, and using this information in conjunction with the phenotypic attributes to obtain more precise clusters of genotypes. The objectives of this study are to present: (1) a retrospective method of analysis for selecting a minimum number of fragments (and markers) from a study needed to produce the same classification of genotypes as that obtained using all the fragments (and markers), and (2) a classification strategy for genotypes that allows the combination of the minimum set of fragments with available phenotypic attributes. Results obtained on seven experimental data sets made up of different plant species, number of individuals per species’ and number of markers, showed that the retrospective analysis did indeed find few relevant fragments (and markers) that best discriminated the genotypes. In two data sets, the classification strategy of combining the information on the relevant minimum fragments with the available morpho-agronomic attributes produced compact and well-differentiated groups of genotypes.

Money matters (I): costs of field and laboratory procedures associated with conventional and marker-assisted maize breeding at CIMMYT

This article presents selected results of a study carried out in Mexico at the International Maize and Wheat Improvement Center (CIMMYT) to compare the cost-effectiveness of conventional and marker-assisted maize breeding. Costs associated with use of conventional and marker-assisted selection (MAS) methods were estimated using a spreadsheet-based budgeting approach. This information was used to compare the cost of using conventional screening and MAS to achieve a well-defined breeding objective—identification of plants carrying a mutant recessive form of the opaque2 gene in maize that is associated with Quality Protein Maize (QPM). In addition to generating empirical cost information that will be of use to CIMMYT research managers, the study produced four important insights. First, for any given breeding project, detailed budget analysis will be needed to determine the cost-effectiveness of MAS relative to conventional selection. Second, direct comparisons of unit costs for MAS methods and conventional selection methods provide useful information for research managers, but factors other than cost are likely to play an important role in driving the choice of screening methods. Third, the choice between MAS and conventional selection may be complicated by the fact that the two are not always direct substitutes. Fourth, when used with empirical data from actual breeding programs, spreadsheet-based budgeting tools can be used by research managers to improve the efficiency of existing protocols and to inform decisions about future technology choices.

Validation of molecular markers for wheat breeding

Five sets of markers were assessed for their usefulness in breeding, two linked to wheat stem rust gene Sr2, several markers linked to a chromosome segment conferring Yr17/Lr37/Sr38 resistance, two reported markers for the linked genes Lr35 andSr39, one for Lr28, and one linked to flour colour. The gene for Sr2 confers adult plant resistance to stem rust (Puccinia graminis f.sp. tritici) and was originally transferred to bread wheat from the tetraploid emmer (‘Yaroslav’) to the cultivars Hope and H-44. The gene is located on the short arm of chromosome 3B and confers a durable adult plant resistance to stem rust usually expressed only in the field. The chromosome segment carrying the Lr37, Sr38, Yr17 resistance genes is located on 2AS and was originally introduced into wheat through an Aegilops ventricosa Triticum persicum cross, followed by a cross to the cultivar Marne (VPM1). The flour colour quantitative trait locus was originally described in a Yarralinka Schomburg cross and is located on chromosome 7A. The primers as originally developed required optimisation for more routine use in a breeding program.

Comparison of molecular markers and coefficients of parentage for the analysis of genetic diversity among spring bread wheat accessions

The comparison of different methods of estimating genetic diversity could define their usefulness in plant breeding and genetic improvement programs. This study evaluates and compares the genetic diversity of 70 spring wheat accessions representing a broad genetic pool based on molecular markers and parentage relationships. The sample was composed of 32 accessions from the International Maize and Wheat Improvement Center (CIMMYT) and 38 from other breeding programs worldwide. Eight AFLP-primer combinations and 37 pairs of SSR primers were used to characterize the accessions and the Coefficients of Parentage (COP) were calculated from registered pedigrees. The average genealogical (COP) similarity (0.09 with a range of 0.0–1.0) was low in comparison to similarity calculated using SSR markers (0.41 with a range of 0.15–0.88) and AFLP markers (0.70 with a range of 0.33–0.98). Correlation between the genealogical similarity matrix (excluding accessions with COPs = 0) and the matrices of genetic similarity based on molecular markers was 0.34≤r≤0.46 (p <0.05). It is concluded that AFLP and SSR markers are generally in agreement with estimates of diversity measured using COPs, especially when complete pedigree data are available. However, markers may provide a more correct estimate due to some unrealistic assumptions made when calculating COPs, such as absence of selection. Furthermore, both COP and marker distances indicate that CIMMYT accessions are different from the worldwide group of accessions.

A diagnostic molecular marker allowing the study of Th. intermedium-derived resistance to BYDV in bread wheat segregating populations

Abstract Barley yellow dwarf (BYD) is the most important viral disease of small cereal grains. True resistance to the disease is not found in wheat (Triticum aestivum L.), but it has been introgressed from Thinopyrum intermedium (Ti) on chromosome 7DL of recombinant wheat lines designated TC. The objectives of our study were to identify a high through-put scoring tool for the presence of the translocated Th. intermedium fragment and to assess its suitability for evaluating resistance to BYDV in segregating populations. Segregation of the Ti fragment was followed in the F2 population of an Anza (bread wheat) by TC14/2*Spear (TC14) cross. Resistance to BYDV isolates PAV-Mex and MAV-Mex in F3, F4, and F5 populations was evaluated under field and/or greenhouse conditions by measuring the virus titers of infected plants using ELISA, and the number of infected plants per plot. The SSR marker gwm37 was polymorphic for the translocation. In F4 lines it was associated with the physical presence of an intact translocation on chromosome 7DL and with low virus titers of BYDV-PAV. Reductions in virus titer of 27% and 55% in the F3 and 18% and 45% in the F5 populations were observed when the fragment was present in the heterozygous and homozygous states, respectively, confirming a dosage effect of the resistance allele. A lower proportion of infected individuals in the field was associated with the presence of the fragment, indicating a mechanism that may interfere with aphid feeding or virus translocation within infected plants. Despite significant differences between groups with and without the fragment, the OD values of infected lines overlapped, and it was not possible to definitively detect the fragment based solely on ELISA. We conclude that gwm37 is a reliable marker for the Ti translocation that will allow efficient detection of the translocation in breeding populations and greatly assist in selecting BYDV-resistant wheats in the absence of the disease.

Genetic mapping of maize streak virus resistance from the Mascarene source : II. Resistance in line CIRAD390 and stability across germplasm

Abstract The streak disease has a major effect on maize in sub-Saharan Africa. Various genetic factors for resistance to the virus have been identified and mapped in several populations; these factors derive from different sources of resistance. We have focused on the Réunion island source and have recently identified several factors in the D211 line. A second very resistant line, CIRAD390, was crossed to the same susceptible parent, B73. The linkage map comprised 124 RFLP markers, of which 79 were common with the D211×B73 map. A row-column design was used to evaluate the resistance to maize streak virus (MSV) of 191 F2:3 families under artificial infestation at two locations: Harare (Zimbabwe) and in Réunion island. Weekly ratings of resistance were taken and disease incidence and severity calculated. QTL analyses were conducted for each scoring date and for the integration over time of the disease scores, of incidence, and of severity. Heritability estimates (71–98%) were as high as for the D211×B73 population. Eight QTLs were detected on chromosomes 1, 2, 3, 5 (two QTLs), 6, 8, and 10. The chr1-QTL explained the highest proportion of phenotypic variation, about 45%. The QTLs on chromosomes 1, 2, and 10 were located in the same chromosomal bin as QTLs for MSV resistance in the D211×B73 population. In a simultaneous fit, QTLs explained together 43–67% of the phenotypic variation. The QTLs on chromosomes 3, 5, and 6 appeared to be specific for one or the other component of the resistance. For the chr3-QTL, resistance was contributed by the susceptible parent. There were significant QTL × environment interactions for some of the variables studied, but QTLs were stable in the two environments. They also appeared to be stable over time. Global gene action ranged from partial dominance to overdominance, except for disease severity. Some additional putative QTLs were also detected. The major QTL on chromosome 1 seemed to be common to the other sources of resistance, namely Tzi4, a tolerant line from IITA, and CML202 from CIMMYT. However, the distribution of the other QTLs within the genome revealed differences in Réunion germplasm and across these other resistance sources. This diversity is of great importance when considering the durability of the resistance.

Identification of QTLs for BYDV tolerance in bread wheat

We searched for QTLs involved in tolerance to barley yellow dwarf (BYD), a serious viral disease of small grain cereals in two wheat populations, Opata × Synthetic (ITMI)and Frontana × INIA66 (F × I), for which marker data had previously been generated. The populations were evaluated in replicated field trials under artificial inoculation with a BYDV-PAV-Mex isolate and under disease-free conditions. Disease symptoms (yellowing, dwarfism and biomass reduction) were visually recorded and agronomic traits (number of tillers,height, biomass, yield and thousand-kernel weight) were measured on five plants per plot. Phenotypic data on all evaluated traits showed normal distribution with high correlation between visual estimates and measured values. Heritabilities were mostly moderate to high in the 114 lines of the ITMI population, and from low to moderate in the 117 lines of the F × I population. QTL analyses were based on genetic maps containing 443 loci for the ITMI population and 317 loci for the F × I population. Using composite interval mapping, 22 QTLs in the ITMI population and seven in the F × I population were detected, explaining9.8–43.3% of total phenotypic variation (σ2P)per agronomic trait in the first population, and 4.1–13.7% in the second. Individual QTLs explained less than 15.8%of σ2P. In the F × I population a minor QTL explaining 7% of σ2P for yellowing was detected on the short arm of 7D, linked to leaf tip necrosis, a morphological marker for linked genes Bdv1, Yr18 andLr34. A QTL consistently detected for several traits on 2D in the ITMI population and on the short arm of group 6 chromosome(6S) in F × I explained 10–15% of σ2P. The large number of QTLs having mostly small effects and the continuous distribution of all evaluated traits confirmed the polygenic nature and complexity of BYD tolerance in wheat.

Is marker-assisted selection cost-effective compared with conventional plant breeding methods? The case of quality protein Maize.

This paper presents the findings of a case study designed to compare the cost of using conventional plant breeding methods with the cost of using a new DNA-based crop selection technique known as marker-assisted selection (MAS). The case study, which was carried out in Mexico at the International Maize and Wheat Improvement Center (CIMMYT), focused on a narrowly-defined breeding objective—transferring the Quality Protein Maize (QPM) phenotype, controlled in part by a mutant allele of a gene called opaque2, from one elite maize inbred line to another elite inbred line. Costs associated with use of conventional breeding methods and MAS for QPM line conversion were estimated using a spreadsheet-based budgeting approach. First, field and laboratory operations involved in conventional and MAS breeding were identified and costed out. Second, representative conventional and MAS breeding schemes were identified. Third, the unique laboratory and field parameters set forth in each breeding scheme were used to calculate the total cost of implementing that particular scheme. Dreher, K., M. Morris, M. Khairallah, J-M. Ribaut, S. Pandey, G. Srinivasan ii ABSTRACT (CONTINUED) Results of the budgeting exercise suggest that currently at CIMMYT, the relative costeffectiveness of conventional breeding methods as compared to MAS for QPM line conversion differs depending on the circumstances. In cases where it is possible to identify segregating materials by visually inspecting ears in the field, conventional breeding methods can be very cost-effective. But in cases where visual selection is not possible, use of molecular markers can lead to significant cost savings. CIMMYT’s experience with MAS parallels the experience of many other breeding programs. Even though MAS has come to play a prominent role in the field of plant breeding, for many practical applications the economics of MAS are still being worked out on a case-by-case basis. The continuing uncertainty concerning the utility of MAS in specific applications should not give rise to undue pessimism, however. Everything that made MAS attractive in the first place still holds true; the key to successfully integrating the technology into applied breeding programs will lie in identifying applications in which molecular markers offer real advantages over conventional breeding methods. MAS should be able to offer significant advantages in cases where phenotypic screening is particularly expensive or difficult, including breeding projects involving multiple genes, recessive genes, late expression of the trait of interest, seasonal considerations, or geographical considerations. In addition to reducing the cost of breeding, MAS also has the potential to generate time savings. Depending on the benefits that a breeding program realizes from earlier release of its breeding products (which typically differ between the private and public sectors), the value of these time savings can be enormous—often justifying the additional cost involved in using MAS. Continuing refinement of molecular marker technologies will make MAS cheaper and more effective in coming years, but at the same time it would be a mistake to assume that marker technologies represent a “silver bullet” solution to every breeding problem. As this case study has revealed, conventional breeding methods still provide a cost-effective option for many types of breeding project, and they will continue to be attractive in the future.

Expression of Thinopyrum intermedium-Derived Barley yellow dwarf virus Resistance in Elite Bread Wheat Backgrounds

ABSTRACT Resistance to Barley yellow dwarf virus (BYDV) is not found in wheat but is available in a Thinopyrum intermedium translocation (Ti) carried on chromosome 7DL of bread wheat recombinant lines. We used one of those lines (TC14/2*Spear) to introgress the Ti into bread wheat cultivars and to determine the influence of wheat backgrounds, with and without known tolerance to BYDV, on the expression of resistance. Two single and three backcross populations, segregating for the presence of the alien fragment, were tested under field conditions and artificial inoculation with BYDV isolates MAV-Mex and PAV-Mex. Lines containing the fragment were identified using the microsatellite marker gwm37. Tillering, biomass, grain yield, thousand-kernel weight, and seed quality were evaluated in inoculated and noninoculated plots. Resistance was assessed by enzyme-linked immunosorbent assay. In early generations, the alien fragment followed expected Mendelian segregation, whereas in the advanced ones a slight bias against its transmission was observed. No positive nor negative effects of Ti on agronomic performance and quality were found. A significant optical density reduction in individuals carrying the fragment was observed after PAV infection in crosses with lines Anza and Baviacora but not with Milan. In addition, the fragment was associated with a lower frequency of infected plants for both PAV and MAV isolates. The reduced yield loss associated with the presence of the translocation was due largely to the lower infection rate.