A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaënsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions and the synthetic amphidiploid grouped separately from most minicore accessions except for COC155, and were eliminated from most subsequent analyses. UPGMA analysis divided the population into four subgroups, two major subgroups representing subspecies fastigiata and hypogaea, a third group containing individuals from each subspecies or possibly of mixed ancestry, and a fourth group, either consisting of COC155 alone if wild species were excluded, or of COC155, the diploid species, and the synthetic amphidiploid. Model-based clustering identified four subgroups- one each for fastigiata and hypogaea subspecies, a third consisting of individuals of both subspecies or of mixed ancestry predominantly from Africa or Asia, and a fourth group, consisting of individuals predominantly of var fastigiata, peruviana, and aequatoriana accessions from South America, including COC155. Analysis of molecular variance (AMOVA) revealed statistically-significant (P < 0.0001) genetic variance of 16.87% among subgroups. A total of 4.85% of SSR marker pairs revealed significant LD (at r² ≥ 0.1). Of the syntenic marker pairs separated by distances < 10 cM, 11–20 cM, 21–50 cM, and > 50 cM, 19.33, 5.19, 6.25 and 5.29% of marker pairs were found in strong LD (P ≤ 0.01), in accord with LD extending to great distances in self pollinated crops. A threshold value of r² > 0.035 was found to distinguish mean r² values of linkage distance groups statistically from the mean r² values of unlinked markers; LD was found to extend to 10 cM over the entire minicore collection by this criterion. However, there were large differences in r² values among marker pairs even among tightly-linked markers. The implications of these findings with regard to the possibility of using association mapping for detection of genome-wide SSR marker-phenotype association are discussed.     

Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin

Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT^® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r ² of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT^® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley.     

Population structure and linkage disequilibrium in oat (<Emphasis Type="Italic">Avena sativa</Emphasis> L.): implications for genome-wide association studies

The level of population structure and the extent of linkage disequilibrium (LD) can have large impacts on the power, resolution, and design of genome-wide association studies (GWAS) in plants. Until recently, the topics of LD and population structure have not been explored in oat due to the lack of a high-throughput, high-density marker system. The objectives of this research were to survey the level of population structure and the extent of LD in oat germplasm and determine their implications for GWAS. In total, 1,205 lines and 402 diversity array technology (DArT) markers were used to explore population structure. Principal component analysis and model-based cluster analysis of these data indicated that, for the lines used in this study, relatively weak population structure exists. To explore LD decay, map distances of 2,225 linked DArT marker pairs were compared with LD (estimated as r ²). Results showed that LD between linked markers decayed rapidly to r ² = 0.2 for marker pairs with a map distance of 1.0 centi-Morgan (cM). For GWAS, we suggest a minimum of one marker every cM, but higher densities of markers should increase marker-QTL association and therefore detection power. Additionally, it was found that LD was relatively consistent across the majority of germplasm clusters. These findings suggest that GWAS in oat can include germplasm with diverse origins and backgrounds. The results from this research demonstrate the feasibility of GWAS and related analyses in oat.     

Association mapping of grain hardness,polyphenol oxidase,total phenolics,amylose content,and β-glucan in US barley breeding germplasm

A renewed interest in breeding barley specifically for food end-uses is being driven by increased consumer interest in healthier foods. We conducted association mapping on physicochemical properties of barley that play a role in food quality and processing including grain hardness, polyphenol oxidase activity, total phenolics, amylose content, and β-glucan. We used 3,069 elite two-row and six-row spring barley breeding lines from eight US breeding programs and 2,041 SNP markers for association mapping. Marker–trait associations were identified using a mixed model that incorporated population structure and kinship. We detected two previously identified QTL for grain hardness on chromosome 2H in the telomeric region of 5H along with two novel regions on 4H and 6H. For amylose content, we detected marker–trait associations on 7H from 0.63 to 30 cM. We detected four regions on chromosomes 1H, 2H, 3H, and 4H associated with polyphenol oxidase activity. The chromosome 2H region co-localized with the two previously mapped polyphenol oxidase genes PPO1 and PPO2, and the regions on chromosomes 1H, 3H, and 4H QTL were novel. For total phenolics, we identified three significant regions on 3H, 4H, and 5H. Two regions on 2H and 7H were associated with β-glucan. Both previously identified and novel QTL are segregating in elite US breeding germplasm. Only three of the 24 SNPs that were associated with traits using either the two-row or six-row mapping panel were identified in both panels. Nine SNPs were detected in the individual two-row or six-row panels that were not detected in the analysis using the complete panel and accounting for population structure. The distribution of favorable alleles at these loci that underpin food quality across the breeding programs suggests several strategies to use markers to improve barley for food uses.     

Analysis of molecular diversity,population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.)

Background

The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles), Principal Coordinate Analysis (PCoA), and analysis of genome-wide linkage disequilibrium.

Results

A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i) geographical regions and (ii) agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD) was estimated as squared correlation of allele frequencies (r²). The values of LD for barley were comparable to other plant species (conifers, poplar, maize). The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r² > 0.05, or up to 10 cM with r² > 0.2. Few loci mapping to different chromosomes showed significant LD with r² > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r² > 0.05 and had higher values of r², although the percentage of intrachromosomal loci pairs in significant LD based on P < 0.001 was 100% in the whole set of varieties, but only 45% in the subgroup of European 2-rowed spring barleys. The value of LD also varied depending on the polymorphism of the loci selected for genotyping. The 17 most polymorphic loci (PIC > 0.80) provided higher LD values as compared to 19 low polymorphic loci (PIC < 0.73) in both structured (all accessions) and non-structured (European 2-rowed spring varieties) barley populations.

Conclusion

A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing similar agronomic characters. LD in barley extended up to 50 cM, and was strongly dependent on the population structure. The data on LD were summarized as a genome-wide LD map for barley.

     

Genome-wide association studies of agronomic and quality traits in a set of German winter barley (Hordeum vulgare L.) cultivars using Diversity Arrays Technology (DArT)

A set of about 100 winter barley (Hordeum vulgare L.) cultivars, comprising diverse and economically important German barley elite germplasm released during the last six decades, was previously genotypically characterized by single nucleotide polymorphism (SNP) markers using the Illumina GoldenGate BeadArray Technology to detect associations with phenotypic data estimated in three-year field trials at 12 locations. In order to identify further associations and to obtain information on whether the marker type influences the outcome of association genetics studies, the set of winter barley cultivars was re-analyzed using Diversity Arrays Technology (DArT) markers. As with the analysis of the SNPs, only polymorphic markers present at an allele frequency >5 % were included to detect associations in a mixed linear model (MLM) approach using the TASSEL software (P?≤?0.001). The population structure and kinship matrix were estimated on 72 simple sequence repeats (SSRs) covering the whole barley genome. The respective average linkage disequilibrium (LD) analyzed with DArT markers was estimated at 5.73 cM. A total of 52 markers gave significant associations with at least one of the traits estimated which, therefore, may be suitable for marker-assisted breeding. In addition, by comparing the results to those generated using the Illumina GoldenGate BeadArray Technology, it turned out that a different number of associations for respective traits is detected, depending on the marker system. However, as only a few of the respective DArT and Illumina markers are present in a common map, no comprehensive comparison of the detected associations was feasible, but some were probably detected in the same chromosomal regions. Because of the identification of additional marker–trait associations, it may be recommended to use both marker techniques in genome-wide association studies.     

Association analysis of seed longevity in rice under conventional and high-temperature germination conditions

Seed longevity varies considerably in cultivated rice, but the underlying mechanism of longevity is not well understood. To measure seed longevity, we performed an aging treatment at 45 °C on seeds maintained at 14 % moisture content for 14 days. We measured the percentage germination of both treated and normal seeds at 25 °C as a control of seed longevity using four replications over 2 years. In total, 140 accessions from a core collection with diverse origins were genotyped using 204 SSR markers, which distributed into 12 chromosomes, to identify marker–trait associations with seed longevity. An analysis of the population structure revealed four subgroups. The r ² values ranged from 0.0 to 0.8901 for all intrachromosomal loci pairs, with an average of 0.0773. Linkage disequilibrium (LD) between linked markers decreased with distance and displayed a substantial drop in LD decay values between 20 and 50 cM. Marker–trait associations were investigated using a mixed linear model approach, considering both population structure (Q) and kinship (K). Twelve marker–trait associations (P < 0.01) were common between the two germination treatments and over the 2-year study, explaining more than 10 % of the total variation. These ten different markers were distributed on five chromosomes. The significant associated SSR markers identified will be useful to seed-bank managers to ensure collections are maintained at high levels of viability to avoid loss of genotypes from the population and for marker-assisted selection.     

A genome-wide association study of malting quality across eight U.S. barley breeding programs

Key message

We report malt quality QTLs relevant to breeding with greater precision than previous mapping studies. The distribution of favorable alleles suggests strategies for marker-assisted breeding and germplasm exchange.

Abstract

This study leverages the breeding data of 1,862 barley breeding lines evaluated in 97 field trials for genome-wide association study of malting quality traits in barley. The mapping panel consisted of six-row and two-row advanced breeding lines from eight breeding populations established at six public breeding programs across the United States. A total of 4,976 grain samples were subjected to micro-malting analysis and mapping of nine quality traits was conducted with 3,072 SNP markers distributed throughout the genome. Association mapping was performed for individual breeding populations and for combined six-row and two-row populations. Only 16 % of the QTL we report here had been detected in prior bi-parental mapping studies. Comparison of the analyses of the combined two-row and six-row panels identified only two QTL regions that were common to both. In total, 108 and 107 significant marker-trait associations were identified in all six-row and all two-row breeding programs, respectively. A total of 102 and 65 marker-trait associations were specific to individual six-row and two-row breeding programs, respectively indicating that most marker-trait associations were breeding population specific. Combining datasets from different breeding program resulted in both the loss of some QTL that were apparent in the analyses of individual programs and the discovery of new QTL not identified in individual programs. This suggests that simply increasing sample size by pooling samples with different breeding history does not necessarily increase the power to detect associations. The genetic architecture of malting quality and the distribution of favorable alleles suggest strategies for marker-assisted selection and germplasm exchange.

     

Improving the efficiency of isolated microspore culture in six-row spring barley: II-exploring novel growth regulators to maximize embryogenesis and reduce albinism

Key message

Two alternative cytokinins, thidiazuron and meta-topoline, were tested in isolated microspore culture on recalcitrant barley genotypes (six-row, spring), and green plant regeneration was improved substantially.

Abstract

Doubled-haploid (DH) plants are coveted in plant breeding and in genetic studies, since they are rapidly obtained and perfectly homozygous. In barley, DHs are produced mainly via androgenesis, and isolated microspore culture (IMC) constitutes the method offering the greatest potential efficiency. However, IMC can often be challenging in some genotypes because of low yield of microspores, low regeneration and high incidence of albinism. Six-row spring-type barleys, the predominant type grown in Eastern Canada, are considered recalcitrant in this regard. Our general objective was to optimize an IMC protocol for DH production in six-row spring barley. In particular, we explored the use of alternative hormones in the induction medium (thidiazuron and dicamba), and in the regeneration medium (meta-topoline). This optimization was performed on two typical six-row spring (ACCA and Léger), a two-row spring (Gobernadora) and a two-row winter (Igri) barley cultivar. When 6-benzyl-aminopurine (BAP) was replaced by a combination of thidiazuron and dicamba in the induction medium, a 5.1-fold increase (P < 0.01) in the production of green plants resulted. This increase was mainly achieved by a reduction of albinism. Moreover, a 2.9-fold increase (P < 0.01) in embryo differentiation into green plants was obtained using meta-topoline instead of BAP in the regeneration medium. Together, these innovations allowed us to achieve a substantial improvement in the efficiency of IMC in this recalcitrant type of barley. These results were later successfully validated using sets of F1s from a six-row spring barley breeding program.     

Improving the efficiency of isolated microspore culture in six-row spring barley: I-optimization of key physical factors

Key message

An improved isolated microspore culture protocol alleviating the recalcitrance typically observed in six-row spring barley was developed by optimizing four key physical factors to increase embryogenesis and reduce albinism.

Abstract

Doubled haploid (DH) plants are completely homozygous individuals that can be generated in just a few months via androgenesis in vitro. DHs are useful tools in genetic research and in plant breeding. Isolated microspore culture (IMC) is the most efficient way to produce DHs, but a strong genotype dependency imposes limitations to its wide application. Six-row, spring barley genotypes are considered as particularly recalcitrant due to a low frequency of embryogenesis and a high rate of albinism. Seeking to develop an efficient IMC protocol for this type of barley, we explored four important factors: (1) the harvest stage of immature spikes, (2) the type of pretreatment applied, (3) the osmotic potential in the induction medium, and (4) the plating density of microspores. This work was first performed using four barley genotypes: two typical six-row spring cultivars (ACCA and Léger), a two-row spring (Gobernadora) and a two-row winter (Igri) cultivar. First, by optimizing the harvest stage for each genotype we obtained a twofold to fourfold increase in the yield of embryogenic microspores. Second, two pretreatments (0.3 M mannitol for 2 days, or a combination of cold and heat over 15 days) both performed significantly better than the commonly used cold pretreatment (28 days at 4 °C). Third, an induction medium-containing mannitol (32 g/l) doubled green plant regeneration. Fourth, a plating density of 10⁶ microspores/ml yielded the highest number of green regenerated plants. Our most important findings were then confirmed using sets of F1s from a six-row, spring-type breeding program.     

Genetic analysis of a two-row × six-row cross of barley using doubled-haploid lines

 A study was conducted on a two-row/six-row cross of barley to (1) determine the yield potential, (2) detect epistasis and genetic correlations, (3) estimate the heritabilities of six agronomic traits, and (4) study the effect of the V locus on the agronomic traits in the barley cross. The effects of five other marker loci (Re2, s, R, Est1, and Est5) on the six agronomic traits were also studied. One hundred and ninety doubled-haploid (DH) lines were derived from a ‘Leger’/CI9831 cross using the bulbosum method. The DH lines and the two parents were tested for grain yield, test weight, seed weight, plant height, lodging, and heading/maturity at two locations in Eastern Canada in 1993. Additive×additive epistasis and genetic correlations were detected for some of the agronomic traits. Many of the heritability estimates were high; however, significant progress in yield improvement would be difficult to achieve because of a low mean yield of the DH lines. Under the growing conditions in Eastern Canada, six-row lines outyielded two-row by 20–27%. Six-row lines, however, were associated with low test weight, low seed weight, and severe lodging. Some two-row lines yielded higher than the two-row parent CI9831, but none of the six-row lines yielded higher than the six-row parent ‘Leger’. The R, s, and Est5 loci were associated with the six agronomic traits, but the Est1 locus was apparently not associated with the agronomic traits. The effect of the Re2 locus was probably due to its close linkage with the V locus. Further studies are needed to determine if superior six-row lines can be developed from two-row/six-row crosses. Received: 19 September 1996 / Accepted: 18 October 1996     

Genome-Wide Association Analysis of Aluminum Tolerance in Cultivated and Tibetan Wild Barley

Tibetan wild barley (Hordeum vulgare L. ssp. spontaneum), originated and grown in harsh enviroment in Tibet, is well-known for its rich germpalsm with high tolerance to abiotic stresses. However, the genetic variation and genes involved in Al tolerance are not totally known for the wild barley. In this study, a genome-wide association analysis (GWAS) was performed by using four root parameters related with Al tolerance and 469 DArT markers on 7 chromosomes within or across 110 Tibetan wild accessions and 56 cultivated cultivars. Population structure and cluster analysis revealed that a wide genetic diversity was present in Tibetan wild barley. Linkage disequilibrium (LD) decayed more rapidly in Tibetan wild barley (9.30 cM) than cultivated barley (11.52 cM), indicating that GWAS may provide higher resolution in the Tibetan group. Two novel Tibetan group-specific loci, bpb-9458 and bpb-8524 were identified, which were associated with relative longest root growth (RLRG), located at 2H and 7H on barely genome, and could explain 12.9% and 9.7% of the phenotypic variation, respectively. Moreover, a common locus bpb-6949, localized 0.8 cM away from a candidate gene HvMATE, was detected in both wild and cultivated barleys, and showed significant association with total root growth (TRG). The present study highlights that Tibetan wild barley could provide elite germplasm novel genes for barley Al-tolerant improvement.     

Linkage Disequilibrium in Salt Tolerant Genotypes of Rice (Oryza sativa L)

Genome wide linkage disequilibrium (LD) was investigated in a set of 32 genotypes representing salt tolerant improved varieties and landraces and six salt sensitive genotypes of rice with 64 microsatellite markers to identify the genomic regions that are associated with salt tolerance in rice. Out of 64 markers analyzed, 36% SSR pairs exhibited significant LD at 0.05. A few regions were identified as targets of selection in 10 chromosomes with high r ² values. The model-based groups from Bayesian clustering analysis are largely consistent with known pedigrees of the lines. The increased percentage of association of SSR loci in the improved varieties indicated the role of selection in linkage disequilibrium especially for salt tolerance. LD was extended as far as 100 cM in the present study. Most of the markers (43.8%) with significant LD values were observed in the genomic regions of reported QTL for salt tolerance in rice.     

DArT markers tightly linked with the <Emphasis Type="Italic">Rfc1</Emphasis> gene controlling restoration of male fertility in the CMS-C system in cultivated rye (<Emphasis Type="Italic">Secale cereale</Emphasis> L.)

The Rfc1 gene controls restoration of male fertility in rye (Secale cereale L.) with sterility-inducing cytoplasm CMS-C. Two populations of recombinant inbred lines (RIL) were used in this study to identify DArT markers located on the 4RL chromosome, in the close vicinity of the Rfc1 gene. In the population developed from the 541×2020LM intercross, numerous markers tightly linked with the restorer gene were identified. This group contained 91 DArT markers and three SCARs additionally analyzed in the study. All these markers were mapped in the distance not exceeding 6 cM from the gene of interest. In the second mapping population (541×Ot1-3 intercross), only 9 DArT markers located closely to the Rfc1 gene were identified. Five of these DArT markers were polymorphic in both populations.     

Patterns of genetic and eco-geographical diversity in Spanish barleys

The pool of Western Mediterranean landraces has been under-utilised for barley breeding so far. The objectives of this study were to assess genetic diversity in a core collection of inbred lines derived from Spanish barley landraces to establish its relationship to barleys from other origins, and to correlate the distribution of diversity with geographical and climatic factors. To this end, 64 SSR were used to evaluate the polymorphism among 225 barley (Hordeum vulgare ssp. vulgare) genotypes, comprising two-row and six-row types. These included 159 landraces from the Spanish barley core collection (SBCC) plus 66 cultivars, mainly from European countries, as a reference set. Out of the 669 alleles generated, a large proportion of them were unique to the six-row Spanish barleys. An analysis of molecular variance revealed a clear genetic divergence between the six-row Spanish barleys and the reference cultivars, whereas this was not evident for the two-row barleys. A model-based clustering analysis identified an underlying population structure, consisting of four main populations for the whole genotype set, and suggested further possible subdivision within two of these populations. Most of the six-row Spanish landraces clustered into two groups that corresponded to geographic regions with contrasting environmental conditions. The existence of wide genetic diversity in Spanish germplasm, possibly related to adaptation to a broad range of environmental conditions, and its divergence from current European cultivars confirm its potential as a new resource for barley breeders, and make the SBCC a valuable tool for the study of adaptation in barley. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Development of an efficient method for assessing resistance to the net type of net blotch (Pyrenophora teres f. teres) in winter barley and mapping of quantitative trait loci for resistance

Breeding for resistance against Pyrenophora teres f. teres in barley is difficult due to the high virulence diversity of the pathogen and the fact that in field trials a simultaneous infection with Rhynchosporium commune, Puccinia hordei or Blumeria graminis f. sp. hordei often takes place. To avoid this, a so-called “summer hill trial” was developed in which winter barley is sown at the beginning of August at optimum conditions for P. teres infection. These trials allowed an unequivocal scoring of P. teres resistance. Using this approach, strong correlations of the results obtained in 3 years at two locations were observed and heritability was estimated at h ² = 0.80 for the doubled haploid (DH) population Uschi × HHOR3073 and h ² = 0.62 for (Post × Viresa) × HHOR9484. In parallel, genetic maps based on DArT, SSR and SNP markers were constructed, comprising 705.7 cM for the DH population Uschi × HHOR3073 and 1,035.8 cM for (Post × Viresa) × HHOR9484. In the population Uschi × HHOR3073, one quantitative trait locus (QTL) was detected on each of chromosomes 2H and 3H and two on chromosome 5H, explaining between 9.4 and 19.0 % of the phenotypic variance. In the population (Post × Viresa) × HHOR9484, three QTL were detected on chromosome 5H and one on chromosome 7H, explaining between 12.6 and 34.7 % of the phenotypic variance. These results show that the new summer hill trial design is best suited to obtain reliable phenotypic data for P. teres resistance under field conditions, as on the one hand already known QTL were confirmed and on the other hand new QTL were detected.     

Discovery of QTLs for water mining and water use efficiency traits in rice under water-limited condition through association mapping

Developing trait introgressed rice cultivars is essential to sustain yield under aerobic conditions. Here, we report DNA markers governing variability in root traits, water use efficiency (WUE) and other biometric traits like total leaf area by association mapping. A set of 173 diverse rice germplasm accessions were phenotyped for root traits in specially designed root structures and WUE using carbon isotope discrimination (Δ¹³C) during the monsoon season (July to October) of two consecutive years (2007 and 2008). The panel was genotyped using 291 SSR markers spanning the entire genome of rice. Root biomass varied between 1.8 and 16.3 g plant^?1 while root length between 22 and 78 cm representing significant genetic variability. Similarly, Δ¹³C varied from 18 to 23 ‰. The SSR markers showed extensive polymorphism with around 73 % of all the markers revealing polymorphism information content values more than 0.5. Model-based structure analysis using the squared-allele frequency correlations revealed six subgroups among the panel with an average LD decay of about 10–20 cM. The Benjamini–Hochberg analysis was carried out to compute the false discovery rate combined with the analysis of effective LD. A total of 82 markers were involved in 175 significant (corrected P values and Q values <0.05) marker–trait associations (MTAs) across experiment 1 and experiment 2 and for the pooled data. Out of these, 22 markers were found to be associated with more than one trait. Common markers with significant associations were discovered for root biomass, total leaf area and total biomass suggesting the interdependency of these traits. Finally, 12 markers showed significant and stable MTAs across the experiments for different traits. An in silico analysis indicated that 45 % of the MTAs overlapped with previously reported QTLs and can be used for QTL introgression through breeding.     

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.     

Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation

Background

Archaeobotanical samples of barley (Hordeum vulgare L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years.

Methodology and Findings

We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure.

Conclusions

The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures.     

Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat

Since the dawn of wheat cytogenetics, chromosome 3B has been known to harbor a gene(s) that, when removed, causes chromosome desynapsis and gametic sterility. The lack of natural genetic diversity for this gene(s) has prevented any attempt to fine map and further characterize it. Here, gamma radiation treatment was used to create artificial diversity for this locus. A total of 696 radiation hybrid lines were genotyped with a custom mini array of 140 DArT markers, selected to evenly span the whole 3B chromosome. The resulting map spanned 2,852 centi Ray with a calculated resolution of 0.384 Mb. Phenotyping for the occurrence of meiotic desynapsis was conducted by measuring the level of gametic sterility as seeds produced per spikelet and pollen viability at booting. Composite interval mapping revealed a single QTL with LOD of 16.2 and r ² of 25.6 % between markers wmc326 and wPt-8983 on the long arm of chromosome 3B. By independent analysis, the location of the QTL was confirmed to be within the deletion bin 3BL7-0.63-1.00 and to correspond to a single gene located ~1.4 Mb away from wPt-8983. The meiotic behavior of lines lacking this gene was characterized cytogenetically to reveal striking similarities with mutants for the dy locus, located on the syntenic chromosome 3 of maize. This represents the first example to date of employing radiation hybrids for QTL analysis. The success achieved by this approach provides an ideal starting point for the final cloning of this interesting gene involved in meiosis of cereals.