High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

As there are numerous pathogen species that cause disease and limit yields of crops, such as wheat (Triticum aestivum), single genes that provide resistance to multiple pathogens are valuable in crop improvement. The mechanistic basis of multi-pathogen resistance is largely unknown. Here we use comparative genomics, mutagenesis and transformation to isolate the wheat Lr67 gene, which confers partial resistance to all three wheat rust pathogen species and powdery mildew. The Lr67 resistance gene encodes a predicted hexose transporter (LR67res) that differs from the susceptible form of the same protein (LR67sus) by two amino acids that are conserved in orthologous hexose transporters. Sugar uptake assays show that LR67sus, and related proteins encoded by homeoalleles, function as high-affinity glucose transporters. LR67res exerts a dominant-negative effect through heterodimerization with these functional transporters to reduce glucose uptake. Alterations in hexose transport in infected leaves may explain its ability to reduce the growth of multiple biotrophic pathogen species.

Linkage disequilibrium can be used for identifying associations between traits of interest and genetic markers. This study used mapped diversity array technology (DArT) markers to find associations with resistance to stem rust, leaf rust, yellow rust, and powdery mildew, plus grain yield in five historical wheat international multienvironment trials from the International Maize and Wheat Improvement Center (CIMMYT). Two linear mixed models were used to assess marker-trait associations incorporating information on population structure and covariance between relatives. An integrated map containing 813 DArT markers and 831 other markers was constructed. Several linkage disequilibrium clusters bearing multiple host plant resistance genes were found. Most of the associated markers were found in genomic regions where previous reports had found genes or quantitative trait loci (QTL) influencing the same traits, providing an independent validation of this approach. In addition, many new chromosome regions for disease resistance and grain yield were identified in the wheat genome. Phenotyping across up to 60 environments and years allowed modeling of genotype 3 environment interaction, thereby making possible the identification of markers contributing to both additive and additive 3 additive interaction effects of traits.A useful new tool for crop genetic improvement is the identification of polymorphic markers associated with phenotypic variation for important traits by means of linkage disequilibrium (LD) between loci ( Thornsberry et al. 2001;Flint-Garcia et al. 2003). A major advantage of this approach over conventional linkage mapping is that it does not require the timeconsuming and expensive generation of specific genetic populations. LD is determined by the physical distance of the loci across chromosomes and has proven useful for dissecting complex traits because it offers fine-scale mapping due to the inclusion of historical recombination (Lynch and Walsh 1998). However, false positive correlation between markers and traits can arise in the absence of physical proximity due to population structure caused by admixture, mating system, and genetic drift or by artificial or natural selection during evolution, domestication, or plant improvement ( Jannink and Walsh 2002). False associations can also be caused by alleles occurring at very low frequencies in the initial population (Breseghello and Sorrells 2006a,b). These factors create LD between loci that are not physically linked and cause a high rate of false positives when relating polymorphic markers to phenotypic trait variation. Thus, separating LD due to physical linkage from LD due to population structure is a critical prerequisite in association analyses.Population structure can be quantified using Bayesian analysis, which has been effective for assigning individuals to subpopulations (Q matrix) using unlinked markers (Pritchard et al. 2000). Other multivariate statistical analyses such as classification (clustering) and ordination (scaling) can al...

Products derived from agricultural biotechnology is fast becoming one of the biggest agricultural trade commodities globally, clothing us, feeding our livestock, and fueling our eco-friendly cars. This exponential growth occurs despite asynchronous regulatory schemes around the world, ranging from moratoriums and prohibitions on genetically modified (GM) organisms, to regulations that treat both conventional and biotech novel plant products under the same regulatory framework. Given the enormous surface area being cultivated, there is no longer a question of acceptance or outright need for biotech crop varieties. Recent recognition of the researchers for the development of a genome editing technique using CRISPR/Cas9 by the Nobel Prize committee is another step closer to developing and cultivating new varieties of agricultural crops. By employing precise, efficient, yet affordable genome editing techniques, new genome edited crops are entering country regulatory schemes for commercialization. Countries which currently dominate in cultivating and exporting GM crops are quickly recognizing different types of gene-edited products by comparing the products to conventionally bred varieties. This nuanced legislative development, first implemented in Argentina, and soon followed by many, shows considerable shifts in the landscape of agricultural biotechnology products. The evolution of the law on gene edited crops demonstrates that the law is not static and must adjust to the mores of society, informed by the experiences of 25 years of cultivation and regulation of GM crops. The crux of this review is a consolidation of the global legislative landscape on GM crops, as it stands, building on earlier works by specifically addressing how gene edited crops will fit into the existing frameworks. This work is the first of its kind to synthesize the applicable regulatory documents across the globe, with a focus on GM crop cultivation, and provides links to original legislation on GM and gene edited crops.

Powdery mildew, caused by Blumeria graminis f. sp. tritici is a major disease of wheat (Triticum aestivum L.) that can be controlled by resistance breeding. The CIMMYT bread wheat line Saar is known for its good level of partial and race non-specific resistance, and the aim of this study was to map QTLs for resistance to powdery mildew in a population of 113 recombinant inbred lines from a cross between Saar and the susceptible line Avocet. The population was tested over 2 years in field trials at two locations in southeastern Norway and once in Beijing, China. SSR markers were screened for association with powdery mildew resistance in a bulked segregant analysis, and linkage maps were created based on selected SSR markers and supplemented with DArT genotyping. The most important QTLs for powdery mildew resistance derived from Saar were located on chromosomes 7DS and 1BL and corresponded to the adult plant rust resistance loci Lr34/Yr18 and Lr46/Yr29. A major QTL was also located on 4BL with resistance contributed by Avocet. Additional QTLs were detected at 3AS and 5AL in the Norwegian testing environments and at 5BS in Beijing. The population was also tested for leaf rust (caused by Puccinia triticina) and stripe rust (caused by P. striiformis f. sp. tritici) resistance and leaf tip necrosis in Mexico. QTLs for these traits were detected on 7DS and 1BL at the same positions as the QTLs for powdery mildew resistance, and confirmed the presence of Lr34/Yr18 and Lr46/Yr29 in Saar. The powdery mildew resistance gene at the Lr34/Yr18 locus has recently been named Pm38. The powdery mildew resistance gene at the Lr46/Yr29 locus is designated as Pm39.

Fusarium head blight (FHB) is a destructive wheat disease of global importance. Resistance breeding depends heavily on the Fhb1 gene. The CIMMYT line Shanghai-3/Catbird (SHA3/CBRD) is a promising source without this gene. A recombinant inbred line (RIL) population from the cross of SHA3/CBRD with the German spring wheat cv. Naxos was evaluated for FHB resistance and related traits in field trials using spray and spawn inoculation in Norway and point inoculation in China. After spray and spawn inoculation, FHB severities were negatively correlated with both anther extrusion (AE) and plant height (PH). The QTL analysis showed that the Rht-B1b dwarfing allele co-localized with a QTL for low AE and increased susceptibility after spawn and spray inoculation. In general, SHA3/CBRD contributed most of the favorable alleles for resistance to severity after spray and spawn inoculation, while Naxos contributed more favorable alleles for reduction in FDK and DON content and resistance to severity after point inoculation. SHA3/CBRD contributed a major resistance QTL close to the centromere on 2DLc affecting FHB severity and DON after all inoculation methods. This QTL was also associated with AE and PH, with high AE and tall alleles contributed by SHA3/CBRD. Several QTL for AE and PH were detected, and low AE or reduced PH was always associated with increased susceptibility after spawn and spray inoculation. Most of the other minor FHB resistance QTL from SHA3/CBRD were associated with AE or PH, while the QTL from Naxos were mostly not. After point inoculation, no other QTL for FHB traits was associated with AE or PH, except the 2DLc QTL which was common across all inoculation methods. Marker-assisted selection based on the 2DLc QTL from SHA3/CBRD combined with phenotypic selection for AE is recommended for resistance breeding based on this valuable source of resistance.

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Grain hardness (“hard” or “soft” kernel texture) is the single most important trait in determining the utilization and marketing of wheat (Triticum aestivum L.). Puroindoline a and b proteins represent the molecular basis for this trait. This study surveyed the prevalence of puroindoline hardness mutations (alleles) among North American spring and winter wheat varieties with emphasis on those that are historically important. Each variety was assessed for kernel texture using the Single Kernel Characterization System; Hardness alleles were defined by puroindoline gene sequence and the presence or absence of puroindoline a protein on polyacrylamide gels. A total of 90 spring wheats were examined: nine were soft and possessed wild‐type (“soft”) puroindoline sequences, 10 were mixed hardness, and the remaining 71 were uniformly hard. Of these hard spring wheats, 18 carried the Pina‐D1b hardness allele (null for puroindoline a protein), 47 the Pinb‐D1b allele (Gly‐46–Ser‐46), and four the Pinb‐D1c allele (Leu‐60–Pro‐60). Two hard spring wheats possessed a new allele, designated Pinb‐D1e, which involves a single nucleotide change in Trp‐39 to a “stop” codon. Lastly, among the spring wheats, a new hardness allele was found in the hard component of the variety ‘Utac’ which was mixed. This allele, Pinb‐D1f, also involved a single nucleotide change such that Trp‐44 became a “stop” codon. A total of 62 winter wheat varieties were examined, of which five were soft and three were of mixed hardness. Of interest, the three mixed hardness wheats were ‘Turkey’, ‘Kharkof’, and ‘Weston’. The hard component of each carried the Pinb‐D1b allele. Of the 54 remaining wheats, all of which were hard, all but two carried this same Pinb‐D1b allele. ‘Chiefkan’ winter wheat carried the same Pinb‐D1e allele as ‘Canadian Red’ and ‘Gehun’ spring wheats. ‘Andrews’ hard red winter wheat possessed a new allele, designated Pinb‐D1g, which was a single nucleotide change in Cys‐56 to a “stop” codon. In conclusion, hard grain phenotype results from one of various mutations in either of the puroindoline proteins. To‐date, seven hardness alleles have been discovered and characterized in hexapoid wheat. All but one occur in the puroindoline b gene coding sequence and result from single nucleotide changes. These molecular markers are useful in characterizing lineages and analyzing ancestral relationships.