An integrated DArT-SSR linkage map of durum wheat

Genetic mapping in durum wheat (Triticum durum Desf.) is constrained by its large genome and allopolyploid nature. We developed a Diversity Arrays Technology (DArT) platform for durum wheat to enable efficient and cost-effective mapping and molecular breeding applications. Genomic representations from 56 durum accessions were used to assemble a DArT genotyping microarray. Microsatellite (SSR) and DArT markers were mapped on a durum wheat recombinant inbred population (176 lines). The integrated DArT-SSR map included 554 loci (162 SSRs and 392 DArT markers) and spanned 2022 cM (5 cM/marker on average). The DArT markers from durum wheat were positioned in respect to anchor SSRs and hexaploid wheat DArT markers. DArT markers compared favourably to SSRs to evaluate genetic relationships among the durum panel, with 1315 DArT polymorphisms found across the accessions. Combining DArT and SSR platforms provides an efficient and rapid method of generating linkage maps in durum wheat.     

Genetic diversity in Chinese modern wheat varieties revealed by microsatellite markers

Genetic diversity of 1680 modern varieties in Chinese candidate core collections was analyzed at 78 SSR loci by fluorescence detection system. A total of 1336 alleles were detected, of which 1253 alleles could be annotated into 71 loci. For these 71 loci, the alleles ranged from 4 to 44 with an average of 17.6, and the PIC values changed from 0.19 to 0.89 with an average of 0.69. (1) In the three genomes of wheat, the average genetic richness was B>A>D, and the genetic diversity indexes were B>D>A. (2) Among the seven homoeologous groups, the average genetic richness was 2=7>3>4>6>5>1, and the genetic diversity indexes were 7>3>2>4>6>5>1. As a whole, group 7 possessed the highest genetic diversity, while groups 1 and 5 were the lowest. (3) In the 21 wheat chromosomes, 7A, 3B and 2D possessed much higher genetic diversity, while 2A, 1B, 4D, 5D and 1D were the lowest. (4) The highest average genetic diversity index existed in varieties bred in the 1950s, and then it declined continually. However, the change tendency of genetic diversity among decades was not greatly sharp. This was further illustrated by changes of the average genetic distance between varieties. In the 1950s it was the largest (0.731). Since the 1960s, it has decreased gradually (0.711, 0.706, 0.696, 0.695). The genetic base of modern varieties is becoming narrower and narrower. This should be given enough attention by breeders and policy makers.     

Genetic and physical mapping of new EST-derived SSRs on the A and B genome chromosomes of wheat

The availability of genetic maps and phenotypic data of segregating populations allows to localize and map agronomically important genes, and to identify closely associated molecular markers to be used in marker-assisted selection and positional cloning. The objective of the present work was to develop a durum wheat intervarietal genetic and physical map based on genomic microsatellite or genomic simple sequence repeats (gSSR) markers and expressed sequence tag (EST)-derived microsatellite (EST-SSR) markers. A set of 122 new EST-SSR loci amplified by 100 primer pairs was genetically mapped on the wheat A and B genome chromosomes. The whole map also comprises 149 gSSR markers amplified by 120 primer pairs used as anchor chromosome loci, two morphological markers (Black colour, Bla1, and spike glaucousness, Ws) and two seed storage protein loci (Gli-A2 and Gli-B2). The majority of SSR markers tested (182) was chromosome-specific. Out of 275 loci 241 loci assembled in 25 linkage groups assigned to the chromosomes of the A and B genome and 34 remained unlinked. A higher percentage of markers (54.4%), localized on the B genome chromosomes, in comparison to 45.6% distributed on the A genome. The whole map covered 1,605 cM. The B genome accounted for 852.2 cM of genetic distance; the A genome basic map spanned 753.1 cM with a minimum length of 46.6 cM for chromosome 5A and a maximum of 156.2 cM for chromosome 3A and an average value of 114.5 cM. The primer sets that amplified two or more loci mapped to homoeologous as well as to non-homoeologous sites. Out of 241 genetically mapped loci 213 (88.4%) were physically mapped by using the nulli-tetrasomic, ditelosomic and a stock of 58 deletion lines dividing the A and B genome chromosomes in 94 bins. No discrepancies concerning marker order were observed but the cytogenetic maps revealed in some cases small genetic distance covered large physical regions. Putative function for mapped SSRs were assigned by searching against GenBank nonredundant database using TBLASTX algorithms.     

Evaluation of the genetic variability of homoeologous group 3 SSRS in bread wheat

Thorough characterization of the genetic variability in bread wheat (Triticum aestivum L.) is important for a better improvement of this key crop and to increase cereal yield in the context of sustainable agriculture to face human needs in the next decades. To study the genetic variability of SSRs on wheat homoeologous group 3 chromosomes, we characterized 38 hexaploid and two tetraploid wheat lines using a set of 165 microsatellites that we cytogenetically assigned to the 17 deletion bins for chromosomes group 3. A comparative analysis of the genetic variability through the PIC value study, allele numbers and SSR lengths indicated that there were no statistically significant differences (p > 0.05) between the three chromosomes of this homoeologous group despite the fact that SSRs from chromosome 3B exhibited slightly more alleles per locus compared to chromosomes 3A and 3D as well as slightly higher PIC values compared to chromosome 3D. However, there was a stronger correlation between SSR length and allele number on the short arms compared to the long aims and the correlation increased from the centromeres toward the telomeres. We did not find statistically significant differences in allele numbers and PIC values for SSRs located in more distal bins on 3A and 3B chromosomes. On the contrary, for chromosome 3D, we observed significant differences (p < 0.05) between the PIC values determined for SSRs assigned to deletion bin 3DL3—0.81–1.00 bin that is located distal compare to the more proximal region (C-3DL3—0.81). These results suggest that recombination which is higher in the telomeric regions does not contribute to increase a lot the variability of the SSRs. The article is published in the original.     

Null alleles for gliadin blocks in bread and durum wheat cultivars

Summary Wheat gliadin proteins are coded by clusters of genes (complex loci) located on the short arms of chromosomes of homoeologous groups 1 and 6 in bread (6x) and durum (4x) wheats. The proteins expressed by the various complex loci have been designated gliadin blocks. In a survey of accessions from the Germplasm Institute (C.N.R., Bari, Italy) collection, several different accessions have been found that lack particular blocks of proteins (null alleles). In some bread wheat accessions, seeds do not express gliadins that are coded by chromosomes 1D and 6A in normal cultivars. Similarly, some durum wheat accessions lack -gliadin components coded for by genes on chromosomes 1A and 1B. The missing proteins do not result from the absence of whole chromosomes, but may be the consequence of partial deletion of these genes at a complex locus or result from their silencing.     

Genome mapping of kernel characteristics in hard red spring wheat breeding lines

Kernel characteristics, particularly kernel weight, kernel size, and grain protein content, are important components of grain yield and quality in wheat. Development of high performing wheat cultivars, with high grain yield and quality, is a major focus in wheat breeding programs worldwide. Here, we report chromosome regions harboring genes that influence kernel weight, kernel diameter, kernel size distribution, grain protein content, and grain yield in hard red spring wheat breeding lines adapted to the Upper Midwest region of the United States. A genetic linkage map composed of 531 SSR and DArT marker loci spanned a distance of 2,505 cM, covering all 21 chromosomes of wheat. Stable QTL clusters influencing kernel weight, kernel diameter, and kernel size distribution were identified on chromosomes 2A, 5B, and 7A. Phenotypic variation explained by individual QTL at these clusters varied from 5 to 20% depending on the trait. A QTL region on chromosome 2B confers an undesirable pleiotropic effect or a repulsion linkage between grain yield (LOD = 6.7; R ² = 18%) and grain protein content (LOD = 6.2; R ² = 13.3%). However, several grain protein and grain yield QTL independent of each other were also identified. Because some of the QTL identified in this study were consistent across environments, DNA markers will provide an opportunity for increasing the frequency of desirable alleles through marker-assisted selection.     

Association mapping of leaf rust response in durum wheat

Resistance to leaf rust (Puccinia triticina Eriks.) is a main objective for durum wheat (Triticum durum Desf.) breeding. Association mapping on germplasm collections is now being used as an additional approach for the discovery and validation of major genes/QTLs. In this study, a collection of 164 elite durum wheat accessions suitable for association mapping has been tested for leaf rust response at the seedling stage and under field conditions (adult plant stage). Seedling tests were carried out with 25 selected isolates from durum wheat, bread wheat and triticale, while field experiments were carried out in artificially inoculated plots in Italy and in Mexico. The collection has been profiled with 225 simple sequence repeat (SSR) loci of known map position and a PCR assay targeting Ppd-A1. Associations showing highly consistent experiment-wise significances across leaf rust isolates and field trials were mainly detected for the 7BL distal chromosome (chr.) region (harbouring Lr14 from cultivar Llareta INIA and QLr.ubo-7B.2 from cultivar Creso) and for two chr. regions located in chrs. 2A and 2B. Additionally, isolate-specific associations and/or associations with smaller effects in the field trials were identified in most of the chromosomes. The chr. 7BL distal region was investigated in detail through haplotyping with 15 SSR markers, revealing that the Creso and Llareta INIA alleles are identical by descent at 6 adjacent SSR loci in the most distal 7BL region spanning 8 cM. Association mapping allowed us to further refine the map location of the Lr14/QLr.ubo-7B.2 resistance gene to the most distal region of the linkage group, tagged by Xcfa2257.2, Xgwm344.2 and Xwmc10. The resistant haplotype is present in a number of accessions (ca. 15% of the accessions included in the collection) from the Italian, CIMMYT and ICARDA breeding programmes. Therefore, this chr. 7BL region can be considered as the most important source of resistance to leaf rust currently exploited by durum breeders in the Mediterranean areas. Furthermore, the field trials at the adult plant stage allowed us to identify marker associations (e.g. chrs. 2BL and 3BS, proximal regions; chr. 7BS, distal region) which suggest the presence of minor QTLs for slow-rusting resistance.     

Association mapping of agronomic traits on chromosome 2A of wheat

Association mapping is a method to test the association between molecular markers and quantitative trait loci (QTL) based on linkage disequilibrium (LD). In this study, the collection of 108 wheat germplasm accessions form China were evaluated for their plant heights, spike length, spikelets per spike, grains per spike, thousand kernel weight and spikelets density in 3 years at three locations. And they were genotyped with 85 SSR markers and 40 EST-SSR markers. The population structure was inferred on the basis of unlinked 48 SSR markers and 40 EST-SSR markers. The extent of LD on chromosome 2A was 2.3 cM. Association of 37 SSR loci on chromosomes 2A with six agronomic traits was analysed with a mixed linear model. A total of 14 SSR loci were significantly associated with agronomic traits. Some of the associated markers were located in the QTL region detected in previous linkage mapping analysis. Our results demonstrated that association mapping can enhance QTL information and achieves higher resolution with short LD extent.     

Analysis of Diversity in Chinese Cultivated Barley with Simple Sequence Repeats: Differences Between Eco-Geographic Populations

The genetic diversity of 116 barley accessions, representing five Chinese eco-geographic populations, was studied using simple sequence repeat (SSR) markers. The 21 SSR loci revealed 128 alleles with an average of 6.1 alleles per locus. The highest values of proportion of polymorphic loci (P) and gene diversity index (He) were obtained in the Northern (P = 1.00; He = 0.60) and the Yangtze River reaches and Southern populations (P = 1.00; He = 0.59). The lowest values were in the populations of the Yellow River reaches (P = 0.86; He = 0.44). The highest average number of alleles per locus (4.52) and number of unique alleles (7) were found in the Qinghai–Tibet plateau population. Cluster analysis revealed that together with the row type, strong eco-geographic variables influenced the classification. Associations of SSR and eco-geographic values were established for 11 SSR loci. Four to six markers were found to discriminate among geographic groups, which may serve as tools for diagnosis of the eco-geographic populations and provide evidence for the adaptive nature of SSR markers.     

Construction of Agropyron Gaertn. genetic linkage maps using a wheat 660K SNP array reveals a homoeologous relationship with the wheat genome

Agropyron Gaertn. (P genome) is a wild relative of wheat that harbours many genetic variations that could be used to increase the genetic diversity of wheat. To agronomically transfer important genes from the P genome to a wheat chromosome by induced homoeologous pairing and recombination, it is necessary to determine the chromosomal relationships between Agropyron and wheat. Here, we report using the wheat 660K single nucleotide polymorphism (SNP) array to genotype a segregating Agropyron F₁ population derived from an interspecific cross between two cross‐pollinated diploid collections ‘Z1842’ [A. cristatum (L.) Beauv.] (male parent) and ‘Z2098’ [A. mongolicum Keng] (female parent) and 35 wheat–A. cristatum addition/substitution lines. Genetic linkage maps were constructed using 913 SNP markers distributed among seven linkage groups spanning 839.7 cM. The average distance between adjacent markers was 1.8 cM. The maps identified the homoeologous relationship between the P genome and wheat and revealed that the P and wheat genomes are collinear and relatively conserved. In addition, obvious rearrangements and introgression spread were observed throughout the P genome compared with the wheat genome. Combined with genotyping data, the complete set of wheat–A. cristatum addition/substitution lines was characterized according to their homoeologous relationships. In this study, the homoeologous relationship between the P genome and wheat was identified using genetic linkage maps, and the detection mean for wheat–A. cristatum introgressions might significantly accelerate the introgression of genetic variation from Agropyron into wheat for exploitation in wheat improvement programmes.     

An estimation of the minimum number of SSR loci needed to reveal genetic relationships in wheat varieties: Information from 96 random accessions with maximized genetic diversity

Genetic relationships among common wheat varieties from the 10 wheat growing regions of China were assessed using SSR markers. The wheat varieties included 33 modern varieties and 63 landraces selected from the national gene bank collection of China. One hundred and four pairs of selected primers detected a total of 802 alleles, of which 234 were specific to A genome, 309 to B genome, and 221 to D genome. The average genetic richness per locus (A _ij /loci) for A, B and D genomes were 6.88, 7.92 and 7.62, respectively. Their average genetic dispersion indices (H _t ) were 0.637, 0.694 and 0.656, respectively. The B genome showed the highest genetic diversity among the three wheat genomes. The landraces had a higher genetic diversity than the modern varieties, and the major difference between the landraces and the modern varieties in China existed in the D genome, followed by B and A genomes. The majority of the accessions (65.6%) had heterogeneity at the 112 loci detected. The highest heterogeneity locus percentages were 9.09 and 12.73 in the modern varieties and the landraces, respectively. SSR data were analyzed with NTSYS-pc software. The genetic similarities between accessions were estimated with the DICE coefficient. The accessions clustered into two groups, the modern varieties and the landraces by the un-weighted pair-group method using arithmetic average (UPGMA). The trend of correlation coefficients between genetic similarity matrices based on different numbers of random alleles and that of 802 alleles showed that 550 alleles were sufficient to construct a robust dendrogram. The separated simulations from six sub-samples revealed that 550 alleles were the minimum number required to confidently determine the genetic relationships. It was shown that the number of alleles (loci) needed do not have a strong association with the number of wheat lines in the sample size. These data suggested that 73 loci with good polymorphism are needed to reflect genetic relationships among accessions with more than 90% certainty. In the dendrogram, most accessions from the same wheat region were clustered together, and those from geographically adjacent regions usually appeared in the same small group. This indicated that genetic diversity of Chinese common wheat has a close association with their geographic distribution and ecological environment.     

Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple-sequence repeats (SSRs)

Fifty one clones isolated from a size-fractionated genomic DNA library of Sorghum bicolor (L.) Moench, that had been probed with four radiolabeled di- and tri-nucleotide oligomers, were sequenced. Fifty of the clones contained one or more simple-sequence repeats (SSRs) [72% of which were (AG/TC) _n SSRs] and, following analysis of the clones, polymerase-chain-reaction primer sets that amplify 38 unique SSR loci were developed. Genotyping of the 38 loci in 18 sorghum accessions, including the parents of a recombinant inbred (RI) mapping population, revealed polymorphism at 36 of the loci among the 18 accessions and at 31 of the loci (not including null alleles at two loci) between the parents of the RI population. All of the latter 31 loci were mapped. The genotypes at 17-mapped SSR loci were assayed in 190 S. bicolor accessions in order to determine δ* _T , the estimated level of allelic differentiation (the estimated probability that two members of a population, chosen at random and without replacement, differ in allelic composition), at each of the loci. The mean δ* _T value determined for S. bicolor overall was 0.89, the range of mean δ* _T values for ten S. bicolor races was from 0.88 to 0.83, and the range of mean δ* _T values for ten working groups (= sub-races) of the race caudatum, with only two exceptions, was from 0.87 to 0.79. The lowest δ* _T values for six of the loci among the ten race-caudatum working groups ranged from 0.86 to 0.70; thus, the probability that different alleles will be present at one or more of these loci in two accessions chosen at random from a working group is > 0.996 when three of the loci are genotyped, and > 0.9999 when all six of the loci are genotyped. The results of this study confirm that most S. bicolor SSR loci are sufficiently polymorphic to be useful in marker- assisted selection programs and they indicate that the levels of polymorphism at some loci are high enough to allow the vast majority of S. bicolor accessions, even accessions within working groups, to be distinguished from one another by determining the genotypes at a small number, perhaps as few as a half-dozen, SSR loci. Received: 13 September 1999 / Accepted: 2 December 1999     

A worldwide bread wheat core collection arrayed in a 384-well plate

Bread wheat (Triticum aestivum), one of the world’s major crops, is genetically very diverse. In order to select a representative sample of the worldwide wheat diversity, 3,942 accessions originating from 73 countries were analysed with a set of 38 genomic simple sequence repeat (SSR) markers. The number of alleles at each locus ranged from 7 to 45 with an average of 23.9 alleles per locus. The 908 alleles detected were used together with passport data to select increasingly large sub-samples that maximised both the number of observed alleles at SSR loci and the number of geographical origins. A final core of 372 accessions (372CC) was selected with this M strategy. All the different geographical areas and more than 98% of the allelic diversity at the 38 polymorphic loci were represented in this core. The method used to build the core was validated, by using a second set of independent markers [44 expressed sequence tag (EST)-SSR markers] on a larger sample of 744 accessions: 96.74% of the alleles observed at these loci had already been captured in the 372CC. So maximizing the diversity with a first set of markers also maximised the diversity at a second independent set of locus. To relate the genetic structure of wheat germplasm to its geographical origins, the two sets of markers were used to compute a dissimilarity matrix between geographical groups. Current worldwide wheat diversity is clearly divided according to wheat’s European and Asian origins, whereas the diversity within each geographical group might be the result of the combined effects of adaptation of an initial germplasm to different environmental conditions and specific breeding practices. Seeds from each accession of the 372CC were multiplied and are now available to the scientific community. The genomic DNA of the 372CC, which can be entirely contained in a 384-deep-well storage plate, will be a useful tool for future studies of wheat genetic diversity. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Development of wheat–<Emphasis Type="Italic">Lophopyrum elongatum</Emphasis> recombinant lines for enhanced sodium ‘exclusion’ during salinity stress

Lophopyrum elongatum (tall wheatgrass), a wild relative of wheat, can be used as a source of novel genes for improving salt tolerance of bread wheat. Sodium ‘exclusion’ is a major physiological mechanism for salt tolerance in a wheat–tall wheatgrass amphiploid, and a large proportion (~50%) for reduced Na⁺ accumulation in the flag leaf, as compared to wheat, was earlier shown to be contributed by genetic effects from substitution of chromosome 3E from tall wheatgrass for wheat chromosomes 3A and 3D. Homoeologous recombination between 3E and wheat chromosomes 3A and 3D was induced using the ph1b mutant, and putative recombinants were identified as having SSR markers specific for tall wheatgrass loci. As many as 14 recombinants with smaller segments of tall wheatgrass chromatin were identified and low-resolution breakpoint analysis was achieved using wheat SSR loci. Seven recombinants were identified to have leaf Na⁺ concentrations similar to those in 3E(3A) or 3E(3D) substitution lines, when grown in 200 mM NaCl in nutrient solution. Phenotypic analysis identified recombinants with introgressions at the distal end on the long arm of homoeologous group 3 chromosomes being responsible for Na⁺ ‘exclusion’. A total of 55 wheat SSR markers mapped to the long arm of homoeologous group 3 markers by genetic and deletion bin mapping were used for high resolution of wheat–tall wheatgrass chromosomal breakpoints in selected recombinants. Molecular marker analysis and genomic in situ hybridisation confirmed the 524-568 recombinant line as containing the smallest introgression of tall wheatgrass chromatin on the distal end of the long arm of wheat chromosome 3A and identified this line as suitable for developing wheat germplasm with Na⁺ ‘exclusion’.     

Mapping of QTLs prolonging the latent period of Puccinia triticina infection in wheat

Slow rusting is considered a crucial component of durable resistance to wheat leaf rust caused by Puccinia triticina and is often expressed in the form of a prolonged latent period. Selection for a longer latent period is considered an effective approach to developing wheat cultivars with improved durable resistance to leaf rust. A recombinant inbred line (RIL) population derived from CI 13227 (long latent period) × Suwon 92 (short latent period) was phenotyped for latent period in two greenhouse experiments in separate years, and amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers were analyzed in the same population. Among the RILs, the frequency distribution for latent period was continuous, and latent period was highly correlated between years (r=0.94, P<0.0001). A quantitative trait locus (QTL) prolonging the latent period of P. triticina, designated as QLrlp.osu-2DS, explained 42.8% and 54.5% of the phenotypic and genetic variance in the two experiments, respectively. QLrlp.osu-2DS was mapped on the distal region of chromosome 2DS. Two other QTLs for latent period, QLrlp.osu-2B and QLrlp.osu-7BL, were localized on chromosome 2B and the long arm of chromosome 7B, respectively. Multiple regression analysis showed that these three QTLs collectively explained 58.0% and 73.8% of the phenotypic and genetic variance over two experiments, respectively. Fourteen RILs that carried all three alleles for long latent period at three AFLP loci flanking QLrlp.osu-2DS, QLrlp.osu-2B, and QLrlp.osu-7BL had a mean latent period of 12.5 days, whereas 13 RILs without any long-latent-period alleles at the corresponding loci had a mean latent period of 7.4 days. Three SSR markers closely linked to these QTLs have potential to be applied in marker-assisted selection for prolonged latent period in wheat.     

Molecular markers for wheat leaf rust resistance gene Lr41

Leaf rust, caused by Puccinia triticina Eriks., is an important foliar disease of common wheat (Triticum aestivum L.) worldwide. Pyramiding several major rust-resistance genes into one adapted cultivar is one strategy for obtaining more durable resistance. Molecular markers linked to these genes are essential tools for gene pyramiding. The rust-resistance gene Lr41 from T. tauschii has been introgressed into chromosome 2D of several wheat cultivars that are currently under commercial production. To discover molecular markers closely linked to Lr41, a set of near-isogenic lines (NILs) of the hard winter wheat cultivar Century were developed through backcrossing. A population of 95 BC₃F_2:6 NILs were evaluated for leaf rust resistance at both seedling and adult plant stages and analyzed with simple sequence repeat (SSR) markers using bulked segregant analysis. Four markers closely linked to Lr41 were identified on chromosome 2DS; the closest marker, Xbarc124, was about 1 cM from Lr41. Physical mapping using Chinese Spring nullitetrasomic and ditelosomic genetic stocks confirmed that markers linked to Lr41 were on chromosome arm 2DS. Marker analysis in a diverse set of wheat germplasm indicated that primers BARC124, GWM210, and GDM35 amplified polymorphic bands between most resistant and susceptible accessions and can be used for marker-assisted selection in breeding programs.     

Identifying loci influencing 1,000-kernel weight in wheat by microsatellite screening for evidence of selection during breeding

Chinese wheat mini core collection (262 accessions) was genotyped at 531 microsatellite loci representing a mean marker density of 5.1 cM. One-thousand-kernel weights (TKW) of lines were measured in five trials (three environments in four growing seasons). Structure analysis based on 42 unlinked SSR loci indicated that the materials formed two sub-populations, viz., landraces and modern varieties. A large difference in TKW (7.08 g, P<0.001) was found between the two sub-groups. Therefore, TKW is a major yield component that was improved in the past 6 decades; it increased from a mean 31.5 g in the 1940s to 44.64 g in the 2000s, representing a 2.19 g increase in each decade. Analyses based on a mixed linear model (MLM), population structure (Q) and relative kinship (K) revealed 22 SSR loci that were significantly associated with mean TKW (MTKW) of the five trials estimated by the best linear unbiased predictor (BLUP) method. They were mainly distributed on chromosomes of homoeologous groups 1, 2, 3, 5 and 7. Six loci, cfa2234-3A, gwm156-3B, barc56-5A, gwm234-5B, wmc17-7A and cfa2257-7A individually explained more than 11.84% of the total phenotypic variation. Favored alleles for breeding at the 22 loci were inferred according to their estimated effects on MTKW based on mean difference of varieties grouped by genotypes. Statistical simulation showed that these favored alleles have additive genetic effects. Frequency changes of alleles at loci associated with TKW are much more dramatic than those at neutral loci between the sub-groups. The numbers of favored alleles in modern varieties indicate there is still considerable genetic potential for their use as markers for genome selection of TKW in wheat breeding. Alleles that can be used globally to increase TKW were inferred according to their distribution by latitude and frequency of changes between landraces and the modern varieties.     

Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat

Genetic variation present in 64 durum wheat accessions was investigated by using three sources of microsatellite (SSR) markers: EST-derived SSRs (EST-SSRs) and two sources of SSRs isolated from total genomic DNA. Out of 245 SSR primer pairs screened, 22 EST-SSRs and 20 genomic-derived SSRs were polymorphic and used for genotyping. The EST-SSR primers produced high quality markers, but had the lowest level of polymorphism (25%) compared to the other two sources of genomic SSR markers (53%). The 42 SSR markers detected 189 polymorphic alleles with an average number of 4.5 alleles per locus. The coefficient of similarity ranged from 0.28 to 0.70 and the estimates of similarity varied when different sources of SSR markers were used to genotype the accessions. This study showed that EST-derived SSR markers developed in bread wheat are polymorphic in durum wheat when assaying loci of the A and B genomes. A minumum of ten EST-SSRs generated a very low probability of identity (0.36×10⁻¹²) indicating that these SSRs have a very high discriminatory power. EST-SSR markers directly sample variation in transcribed regions of the genome, which may enhance their value in marker-assisted selection, comparative genetic analysis and for exploiting wheat genetic resources by providing a more-direct estimate of functional diversity. Received: 19 December 2000 / Accepted: 17 April 2001