Rapid genetic gain was achieved for cooking time in common bean based on multivariate genomic analysis, but forward predictive ability was low and phenotyping remains essential to secure genetic gain. Common beans (Phaseolus vulgaris L.) are a major source of protein and energy in sub-Saharan Africa, but their long cooking time (CKT) imposes social, economic, environmental and health burdens. This study aimed to accelerate genetic gain for shorter CKT while maintaining or improving other seed traits such as seed iron (Fe) and zinc (Zn) content, water absorption capacity (WAC) and 100-seed weight (SW100) across rapid cycles of early-generation genomic selection. Two related founder populations were selected from the African bean panel and intercrossed in 2020 (population A) and 2021 (population B), followed by rapid two-year cycles of augmented S0-derived family selection based on an index and optimal contributions selection. Best linear unbiased predictions (BLUPs) of breeding values were obtained from pedigree (ABLUP), genomic (GBLUP) and single-step (HBLUP) multivariate linear mixed model analysis across two cycles. Realised genetic gain from cycle 1 to cycle 2 was high for CKT (average -8.0 min y−1) and favourably correlated with WAC (average + 7.7

Common beans ( Phaseolus vulgaris L.) are a major source of protein and energy in sub-Saharan Africa, but their long cooking time (CKT) imposes social, economic, environmental and health burdens. This study aimed to accelerate genetic gain for shorter CKT while maintaining or improving other seed traits such as seed iron (Fe) and zinc (Zn) content, water absorption capacity (WAC) and 100-seed weight (SW100) across rapid cycles of early-generation genomic selection. Two related founder populations were selected from the African bean panel and intercrossed in 2020 (population A) and 2021 (population B), followed by rapid two-year cycles of augmented S 0 -derived family selection. Best linear unbiased predictions (BLUPs) of breeding values were obtained from pedigree, genomic and single-step (combined pedigree and genomic) multivariate linear mixed model analysis across two cycles. Shorter CKT was correlated with higher WAC but lower Fe and Zn. Realised genetic gain from cycle 1 to cycle 2 was high for CKT (average -8.0 min y -1 ) and WAC (average +7.7% y -1 ), but was accompanied by small decreases in Fe, Zn and SW100. Genomic and single-step models resulted in high accuracy of BLUPs and moderate predictive ability across breeding cycles. The predicted genomic BLUPs for CKT in cycle 2B S 0 seedlings were strongly correlated by rank with their realised genomic BLUPs in S 0 -derived self bulks one year later, especially in a leave-one-trait-out approach in single-step multivariate genomic analysis. Indirect selection in S 0 progeny plants based on correlated and easy-to-measure traits may increase the rate of genetic gain in all traits.

Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper.

Common bean (Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding values (GEBV) for grain yield (GY), CKT, Fe, and Zn in an African bean panel of 358 genotypes in a two-stage analysis. In Stage 1, best linear unbiased estimates (BLUE) for each trait were obtained from 898 genotypes across 33 field trials in East Africa. In Stage 2, BLUE in a training population of 141 genotypes were used in a multivariate genomic analysis with genome-wide single nucleotide polymorphism data from the African bean panel. Moderate to high genomic heritability was found for GY (0.45 ± 0.10), CKT (0.50 ± 0.15), Fe (0.57 ± 0.12), and Zn (0.61 ± 0.13). There were significant favorable genetic correlations between Fe and Zn (0.91 ± 0.06), GY and Fe (0.66 ± 0.17), GY and Zn (0.44 ± 0.19), CKT and Fe (-0.57 ± 0.21), and CKT and Zn (-0.67 ± 0.20). Optimal contributions selection (OCS), based on economic index of weighted GEBV for each trait, was used to design crossing within four market groups relevant to East Africa. Progeny were predicted by OCS to increase in mean GY by 12.4%, decrease in mean CKT by 9.3%, and increase in mean Fe and Zn content by 6.9 and 4.6%, respectively, with low achieved coancestry of 0.032. Genomic selection with OCS will accelerate breeding of high-yielding, biofortified, and rapid cooking African common bean cultivars.

Key message Wheat blast resistance in Caninde#1 is controlled by a major QTL on 2NS/2AS translocation and multiple minor QTL in an additive mode. Abstract Wheat blast (WB) is a devastating disease in South America, and it recently also emerged in Bangladesh. Host resistance to WB has relied heavily on the 2NS/2AS translocation, but the responsible QTL has not been mapped and its phenotypic effects in different environments have not been reported. In the current study, a recombinant inbred line population with 298 progenies was generated, with the female and male parents being Caninde#1 (with 2NS) and Alondra (without 2NS), respectively. Phenotyping was carried out in two locations in Bolivia, namely Quirusillas and Okinawa, and one location in Bangladesh, Jashore, with two sowing dates in each of the two cropping seasons in each location, during the years 2017–2019. Genotyping was performed with the DArTseq® technology along with five previously reported STS markers in the 2NS region. QTL mapping identified a major and consistent QTL on 2NS/2AS region, explaining between 22.4 and 50.1% of the phenotypic variation in different environments. Additional QTL were detected on chromosomes 1AS, 2BL, 3AL, 4BS, 4DL and 7BS, all additive to the 2NS QTL and showing phenotypic effects less than 10%. Two codominant STS markers, WGGB156 and WGGB159 , were linked proximally to the 2NS/2AS QTL with a genetic distance of 0.9 cM, being potentially useful in marker-assisted selection.

BACKGROUND:Wheat is the most important staple crop in Afghanistan and accounts for the main part of cereal production. However, wheat production has been unstable during the last decades and the country depends on seed imports. Wheat research in Afghanistan has emphasized releases of new, high-yielding and disease resistant varieties but rates of adoption of improved varieties are uncertain. We applied DNA fingerprinting to assess wheat varieties grown in farmers' fields in four Afghan provinces.RESULTS:Of 560 samples collected from farmers' fields during the 2015-16 cropping season, 74% were identified as varieties released after 2000, which was more than the number reported by farmers and indicates the general prevalence of use of improved varieties, albeit unknowingly. At the same time, we found that local varieties and landraces have been replaced and were grown by 4% fewer farmers than previously reported. In 309 cases (58.5%), farmers correctly identified the variety they were growing, while in 219 cases (41.5%) farmers did not. We also established a reference library of released varieties, elite breeding lines, and Afghan landraces, which confirms the greater genetic diversity of the landraces and their potential importance as a genetic resource.CONCLUSIONS:Our study is the first in wheat to apply DNA fingerprinting at scale for an accurate assessment of wheat varietal adoption and our findings point up the importance of DNA fingerprinting for accuracy in varietal adoption studies.

Table S1. Initial list and source of 1581 entries used for data analyses, including 965 reference varities, 650 farmersâ samples and 56 technical replicates. Table S2. Pairwise identity by state (IBS) similarities among technical replicates. Table S3. Predicted and with DNA fingerprinting re-identified cultivars from farmers field in Afghanistan. Table S4. Informative markers applied across collected Afghan field samples. Table S5. Presence of genes in identified wheat varieties in Afghan farmers fields. Table S6. Established Afghan reference library. Table S7. Diversity indicies of germplasm groups represented in the established Afghan reference library. Table S8. Varieties released in Afghanistan since 2000. (XLSX 189 kb)

Since 2012, Australian support has resulted in the release of 23 wheat varieties by Afghanistan’s National Varietal Release Committee (NVRC). These varieties deliver both improved yield and disease tolerance. A 2015/16 farmer survey confirmed that farmers were indeed sharing seed with an average of three relatives/neighbours – although with no indication of how much seed was shared. This uncertainty regarding the adoption of new varieties has been intended to resolve by a recent DNA assessments of seed collected in 2015/16 that shows the general prevalence of the new varieties across 600 surveyed farms.

Tobacco (Nicotiana tabacum) is one of the most economically important nonfood crops, and flue-cured tobacco accounts for approximately 80% of world tobacco production. An extremely narrow genetic diversity in the tobacco pool has led to a low efficiency of PCR-based molecular markers (such as AFLP and SSR). Diversity Arrays Technology (DArT) is a high-throughput hybridisation-based marker system that has been developed in many plants including wheat, which, like tobacco, has a complex genome. In this study, we developed a tobacco DArT chip that included 7680 representative sequence tags based on typical tobacco accessions. The 1076 DArT markers of flue-cured tobacco were identified and most (82.1%) of their polymorphism information contents (PICs) were greater than 0.4. An integrated linkage map that included 851 markers (238 DArT and 613 SSR), which is the highest density map of flue-cured tobacco to date, was constructed. This chip-based DArT system provides an alternative in high-throughput marker genotyping for tobacco.

Analysis of the extent of genetic variation within genetic resources is important for diversity preservation and also for breeders who exploit it. We investigated the recently introduced molecular marker technique of DNA diversity array technology (DArT), with the objective of characterising diversity in the likely relatively narrow genetic background of Czech malting barley cultivars. A total of 94 obsolete or registered barley cultivars and some hulless barley lines primarily of Czech origin were characterised by DArT analysis. A total of 271 polymorphic marker alleles were revealed across the analysed set of accessions, 37 of which were identified as being overrepresented; the other 234 markers were used for further analysis. The average dissimilarity value within the analysed set of accessions was 0.692. To assess how well DArT is suited for individual barley characteristic evaluation, available agronomical data from three yield field trials were used. Out of 94 barley genotypes used in the field trials that were assessed by DArTs, 41 have been grown over time as malting cultivars in the region. Similarity matrices based on Gower’s coefficient for mixed data and simple matching coefficient were used to compare DaRT and agronomical results. We demonstrate that a DArT-based similarity matrix and an agronomical data-based similarity matrix correlated well. To assess the genetic structure of the entire collection, K-means and simple matching coefficient clustering were used. Statistical analysis confirmed the power of the DArT system, in fact they efficiently grouped old genetic resources and modern cultivars in the expected way. Our results show that the level of genetic diversity has not changed substantially over time, but significant shifts in allelic frequency have occurred. In addition, a DArT-based dendrogram and principal component analysis (PCA) plots clearly demonstrated the impact of breeding practices on the diversity of Czech spring malting barley cultivars over time.

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.

In the last 20 years, we have observed an exponential growth of the DNA sequence data and simular increase in the volume of DNA polymorphism data generated by numerous molecular marker technologies. Most of the investment, and therefore progress, concentrated on human genome and genomes of selected model species. Diversity Arrays Technology (DArT), developed over a decade ago, was among the first "democratizing" genotyping technologies, as its performance was primarily driven by the level of DNA sequence variation in the species rather than by the level of financial investment. DArT also proved more robust to genome size and ploidy-level differences among approximately 60 organisms for which DArT was developed to date compared to other high-throughput genotyping technologies. The success of DArT in a number of organisms, including a wide range of "orphan crops," can be attributed to the simplicity of underlying concepts: DArT combines genome complexity reduction methods enriching for genic regions with a highly parallel assay readout on a number of "open-access" microarray platforms. The quantitative nature of the assay enabled a number of applications in which allelic frequencies can be estimated from DArT arrays. A typical DArT assay tests for polymorphism tens of thousands of genomic loci with the final number of markers reported (hundreds to thousands) reflecting the level of DNA sequence variation in the tested loci. Detailed DArT methods, protocols, and a range of their application examples as well as DArT's evolution path are presented.

Diversity arrays technology (DArT) genomic libraries were developed from H. chilense accessions to support robust genotyping of this species and a novel crop comprising H. chilense genome (e.g., tritordeums). Over 11,000 DArT clones were obtained using two complexity reduction methods. A subset of 2,209 DArT markers was identified on the arrays containing these clones as polymorphic between parents and segregating in a population of 92 recombinant inbred lines (RIL) developed from the cross between H. chilense accessions H1 and H7. Using the segregation data a high-density map of 1,503 cM was constructed with average inter-bin density of 2.33 cM. A subset of DArT markers was also mapped physically using a set of wheat-H. chilense chromosome addition lines. It allowed the unambiguous assignment of linkage groups to chromosomes. Four segregation distortion regions (SDRs) were found on the chromosomes 2H(ch), 3H(ch) and 5H(ch) in agreement with previous findings in barley. The new map improves the genome coverage of previous H. chilense maps. H. chilense-derived DArT markers will enable further genetic studies in ongoing projects on hybrid wheat, seed carotenoid content improvement or tritordeum breeding program. Besides, the genetic map reported here will be very useful as the basis to develop comparative genomics studies with barley and model species.

Isolated microspore culture based androgenesis is being used for production of haploid (H) and doubled haploid (DH) plants in wheat. This technique can facilitate the efficiency of wheat breeding and genetic mapping as well as research in functional genomics and gene expression. Until now there was no report of microspore culture in Nebraskan winter wheat varieties. The objectives of the present report were to (1) study the androgenic response of Nebraskan winter wheat varieties and (2) establish efficient procedure for green DH plant regeneration. Three Nebraskan winter varieties (Anton, Antelope, and Camelot) were used. The spikes were collected from greenhouse-grown plants when microspores were at mid-late to late-uninucleate stage. For each batch of pretreatment, anthers from 16 spikes were pretreated in solution B at 25°C for 4–5 days followed by microspores isolation (no cold pretreatment). For cold pretreatment, anthers were incubated at 4°C for additional five days. The numbers of embryogenic microspores, multicellular, and embryo-like structures were recorded and analyzed. Compared to no cold pretreatment, a cold pretreatment increased the number of embryogenic microspores significantly in Anton by two fold, but no significant differences between the two pretreatments were observed in Camelot and Antelope. In vitro development of microspores into multicellular and embryo-like structures were quicker in Camelot than Anton and Antelope. The green plants were regenerated in all three varieties following both cold and no cold pretreatment. The number of regenerated green plants per batch of pretreatment was four (no cold) and eight (cold) in case of Antelope. However, for Anton and Camelot, there was one green plant per batch in both the cold and no cold treatments. It seems that higher number of embryogenic microspores due to cold pretreatment in Anton was not regenerated into proportionate number of green plants. An experiment is under progress to determine a similar response in Camelot and Antelope. This is the first report of androgenic response of Nebraskan winter wheat varieties. We believe that this method will be a beneficial tool in our wheat breeding efforts. However green plant regeneration frequency needs to be increased for cost-effective use.

DArT technology was applied to a tetraploid (2n = 4x = 28) L. multiflorum´F. glaucescens hybrid lineage over ten generations. By selecting 151 Lolium- and 210 Festuca-specific DArT markers among the 3,884 ones developed by Kopecký et al. (Development and mapping of DArT markers within the Festuca–Lolium complex, BMC Genomics 10:473, 2009), it is shown that DArT polymorphism is well consistent with the history of the plant material and the events in relation with interspecific hybridisation: amphiploidisation, introgression into 4x- and 2x-L. multiflorum, reduction of effective size, chromosome mapping as well as parent-specific response to summer water deficit. In this respect, frequency of Festuca markers within a 4x-BC1 population was found to have increased on average by 2.4 % among plants having survived in sward after summer while frequency decreased by 10.2 % after three generations of seed multiplication from the initial polycross of BC1 parents.

BACKGROUND:The uneven distribution of recombination across the length of chromosomes results in inaccurate estimates of genetic to physical distances. In wheat (Triticum aestivum L.) chromosome 3B, it has been estimated that 90% of the cross over events occur in distal sub-telomeric regions representing 40% of the chromosome. Radiation hybrid (RH) mapping which does not rely on recombination is a strategy to map genomes and has been widely employed in animal species and more recently in some plants. RH maps have been proposed to provide i) higher and ii) more uniform resolution than genetic maps, and iii) to be independent of the distribution patterns observed for meiotic recombination. An in vivo RH panel was generated for mapping chromosome 3B of wheat in an attempt to provide a complete scaffold for this ~1 Gb segment of the genome and compare the resolution to previous genetic maps.RESULTS:A high density RH map with 541 marker loci anchored to chromosome 3B spanning a total distance of 1871.9 cR was generated. Detailed comparisons with a genetic map of similar quality confirmed that i) the overall resolution of the RH map was 10.5 fold higher and ii) six fold more uniform. A significant interaction (r = 0.879 at p = 0.01) was observed between the DNA repair mechanism and the distribution of crossing-over events. This observation could be explained by accepting the possibility that the DNA repair mechanism in somatic cells is affected by the chromatin state in a way similar to the effect that chromatin state has on recombination frequencies in gametic cells.CONCLUSIONS:The RH data presented here support for the first time in vivo the hypothesis of non-casual interaction between recombination hot-spots and DNA repair. Further, two major hypotheses are presented on how chromatin compactness could affect the DNA repair mechanism. Since the initial RH application 37 years ago, we were able to show for the first time that the iii) third hypothesis of RH mapping might not be entirely correct.

Triticale (X Triticosecale Wittm.) is a hybrid derived by crossing wheat (Triticum sp.) and rye (Secale sp.). Till date, only a limited number of simple sequence repeat (SSRs) markers have been used in triticale molecular analyses and there is a need to identify dedicated high-throughput molecular markers to better exploit this crop. The objective of this study was to develop and evaluate diversity arrays technology (DArT) markers in triticale. DArT marker technology offers a high level of multiplexing. Development of new markers from triticale accessions was combined with mining the large collection of previously developed markers in rye and wheat. Three genotyping arrays were used to analyze a collection of 144 triticale accessions. The polymorphism level ranged from 8.6 to 23.8% for wheat and rye DArT markers, respectively. Among the polymorphic markers, rye markers were the most abundant (3,109) followed by wheat (2,214) and triticale (719). The mean polymorphism information content values were 0.34 for rye DArT markers and 0.37 for those from triticale and wheat. High correlation was observed between similarity matrices derived from rye, triticale, wheat and combined marker sets, as well as for the cophenetic values matrices. Cluster analysis revealed genetic relationships among the accessions consistent with the agronomic and pedigree information available. The newly developed triticale DArT markers as well as those originated from rye and wheat provide high quality markers that can be used for diversity analyses and might be exploited in a range of molecular breeding and genomics applications in triticale.