Huw Jones

Population-Based Resequencing Reveals That the Flowering Time Adaptation of Cultivated Barley Originated East of the Fertile Crescent

Gene resequencing and association analysis present new opportunities to study the evolution of adaptive traits in crop plants. Here we apply these tools to an extensive set of barley accessions to identify a component of the molecular basis of the flowering time adaptation, a trait critical to plant survival. Using an association-based study to relate variation in flowering time to sequence-based polymorphisms in the Ppd-H1 gene, we identify a causative polymorphism (SNP48) that accounts for the observed variation in barley flowering time. This polymorphism also shows latitude-dependent geographical distribution, consistent with the expected clinal variation in phenotype with the nonresponsive form predominating in the north. Networks, genealogies, and phylogenetic trees drawn for the Ppd-H1 haplotypes reveal population structure both in wild barley and in domesticated barley landraces. The spatial distribution of these population groups indicates that phylogeographical analysis of European landraces can provide information relevant to the Neolithic spread of barley cultivation and also has implications for the origins of domesticated barley, including those with the nonresponsive ppd-H1 phenotype. Haplotypes containing the nonresponsive version of SNP48 are present in wild barley accessions, indicating that the nonresponsive phenotype of European landraces originated in wild barley. The wild accessions whose nonresponsive haplotypes are most closely similar to those of landraces are found in Iran, within a region suggested as an area for domestication of barley east of the Fertile Crescent but which has previously been thought to have contributed relatively little to the diversity of European cultivars.

CorrSieve: software for summarizing and evaluating Structure output

The clustering software Structure has been used extensively to infer population structure in natural populations from multilocus genotype data. Determining meaningful values of K, the assumed number of subpopulations is one of the primary challenges of making biological inferences from Structure data. The package CorrSieve summarizes Structure output and performs a number of tests, including both previously reported methods and novel ones, to help determine meaningful values of K.

Approaches and constraints of using existing landrace and extant plant material to understand agricultural spread in prehistory

The potential for the phylogeographical analysis of cereal landraces to determine the initial patterns of agricultural spread through Europe is discussed in relation to two of the first cereals to be domesticated, emmer wheat (Triticum turgidum subsp. dicoccum) and barley (Hordeum vulgare). Extant landraces available from germplasm collections have a patchy distribution, largely being confined to regions of rugged upland topography, and the phylogeographical patterns observed may be due to ‘overstamping’ by more recent crop movements. Phylogeographical studies of non-viable historical landrace material held in herbarium and old seed collections and found in historical buildings have the potential to fill in the gaps in time and space. We explore the importance of precise geographical provenance and the limitations of this in extant and historical material. Additionally, we consider the effect of various chemicals and the preservation of DNA in the historical material.

Tetraploid wheat landraces in the Mediterranean basin: taxonomy, evolution and genetic diversity.

The geographic distribution of genetic diversity and the population structure of tetraploid wheat landraces in the Mediterranean basin has received relatively little attention. This is complicated by the lack of consensus concerning the taxonomy of tetraploid wheats and by unresolved questions regarding the domestication and spread of naked wheats. These knowledge gaps hinder crop diversity conservation efforts and plant breeding programmes. We investigated genetic diversity and population structure in tetraploid wheats (wild emmer, emmer, rivet and durum) using nuclear and chloroplast simple sequence repeats, functional variations and insertion site-based polymorphisms. Emmer and wild emmer constitute a genetically distinct population from durum and rivet, the latter seeming to share a common gene pool. Our population structure and genetic diversity data suggest a dynamic history of introduction and extinction of genotypes in the Mediterranean fields.

Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces

BackgroundUnderstanding the evolution of cultivated barley is important for two reasons. First, the evolutionary relationships between different landraces might provide information on the spread and subsequent development of barley cultivation, including the adaptation of the crop to new environments and its response to human selection. Second, evolutionary information would enable landraces with similar traits but different genetic backgrounds to be identified, providing alternative strategies for the introduction of these traits into modern germplasm.ResultsThe evolutionary relationships between 651 barley landraces were inferred from the genotypes for 24 microsatellites. The landraces could be divided into nine populations, each with a different geographical distribution. Comparisons with ear row number, caryopsis structure, seasonal growth habit and flowering time revealed a degree of association between population structure and phenotype, and analysis of climate variables indicated that the landraces are adapted, at least to some extent, to their environment. Human selection and/or environmental adaptation may therefore have played a role in the origin and/or maintenance of one or more of the barley landrace populations. There was also evidence that at least some of the population structure derived from geographical partitioning set up during the initial spread of barley cultivation into Europe, or reflected the later introduction of novel varieties. In particular, three closely-related populations were made up almost entirely of plants with the daylength nonresponsive version of the photoperiod response gene PPD-H1, conferring adaptation to the long annual growth season of northern Europe. These three populations probably originated in the eastern Fertile Crescent and entered Europe after the initial spread of agriculture.ConclusionsThe discovery of population structure, combined with knowledge of associated phenotypes and environmental adaptations, enables a rational approach to identification of landraces that might be used as sources of germplasm for breeding programs. The population structure also enables hypotheses concerning the prehistoric spread and development of agriculture to be addressed.

The cosmopolitan maternal heritage of the Thoroughbred racehorse breed shows a significant contribution from British and Irish native mares

The paternal origins of Thoroughbred racehorses trace back to a handful of Middle Eastern stallions, imported to the British Isles during the seventeenth century. Yet, few details of the foundation mares were recorded, in many cases not even their names (several different maternal lineages trace back to ‘A Royal Mare’). This has fuelled intense speculation over their origins. We examined mitochondrial DNA from 1929 horses to determine the origin of Thoroughbred foundation mares. There is no evidence to support exclusive Arab maternal origins as some historical records have suggested, or a significant importation of Oriental mares (the term used in historic records to refer to Middle East and western Asian breeds including Arab, Akhal-Teke, Barb and Caspian). Instead, we show that Thoroughbred foundation mares had a cosmopolitan European heritage with a far greater contribution from British and Irish Native mares than previously recognized.

Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.)

The deployment of genetic markers is of interest in crop assessment and breeding programmes, due to the potential savings in cost and time afforded. As part of the internationally recognised framework for the awarding of Plant Breeders’ Rights (PBR), new barley variety submissions are evaluated using a suite of morphological traits to ensure they are distinct, uniform and stable (DUS) in comparison to all previous submissions. Increasing knowledge of the genetic control of many of these traits provides the opportunity to assess the potential of deploying diagnostic/perfect genetic markers in place of phenotypic assessment. Here, we identify a suite of 25 genetic markers assaying for 14 DUS traits, and implement them using a single genotyping platform (KASPar). Using a panel of 169 UK barley varieties, we show that phenotypic state at three of these traits can be perfectly predicted by genotype. Predictive values for an additional nine traits ranged from 81 to 99xa0%. Finally, by comparison of varietal discrimination based on phenotype and genotype resulted in correlation of 0.72, indicating that deployment of molecular markers for varietal discrimination could be feasible in the near future. Due to the flexibility of the genotyping platform used, the genetic markers described here can be used in any number or combination, in-house or by outsourcing, allowing flexible deployment by users. These markers are likely to find application where tracking of specific alleles is required in breeding programmes, or for potential use within national assessment programmes for the awarding of PBRs.

Waxy Phenotype Evolution in the Allotetraploid Cereal Broomcorn Millet: Mutations at the GBSSI Locus in Their Functional and Phylogenetic Context

Waxy mutants, in which endosperm starch contains ∼100% amylopectin rather than the wild-type composition of ∼70% amylopectin and ∼30% amylose, occur in many domesticated cereals. The cultivation of waxy varieties is concentrated in east Asia, where there is a culinary preference for glutinous-textured foods that may have developed from ancient food processing traditions. The waxy phenotype results from mutations in the GBSSI gene, which catalyzes amylose synthesis. Broomcorn or proso millet (Panicum miliaceum L.) is one of the world’s oldest cultivated cereals, which spread across Eurasia early in prehistory. Recent phylogeographic analysis has shown strong genetic structuring that likely reflects ancient expansion patterns. Broomcorn millet is highly unusual in being an allotetraploid cereal with fully waxy varieties. Previous work characterized two homeologous GBSSI loci, with multiple alleles at each, but could not determine whether both loci contributed to GBSSI function. We first tested the relative contribution of the two GBSSI loci to amylose synthesis and second tested the association between GBSSI alleles and phylogeographic structure inferred from simple sequence repeats (SSRs). We evaluated the phenotype of all known GBSSI genotypes in broomcorn millet by assaying starch composition and protein function. The results showed that the GBSSI-S locus is the major locus controlling endosperm amylose content, and the GBSSI-L locus has strongly reduced synthesis capacity. We genotyped 178 individuals from landraces from across Eurasia for the 2 GBSSI and 16 SSR loci and analyzed phylogeographic structuring and the geographic and phylogenetic distribution of GBSSI alleles. We found that GBSSI alleles have distinct spatial distributions and strong associations with particular genetic clusters defined by SSRs. The combination of alleles that results in a partially waxy phenotype does not exist in landrace populations. Our data suggest that broomcorn millet is a system in the process of becoming diploidized for the GBSSI locus responsible for grain amylose. Mutant alleles show some exchange between genetic groups, which was favored by selection for the waxy phenotype in particular regions. Partially waxy phenotypes were probably selected against—this unexpected finding shows that better understanding is needed of the human biology of this phenomenon that distinguishes cereal use in eastern and western cultures.

A baseline study of vicine–convicine levels in faba bean ( Vicia faba L.) germplasm

Vicine and convicine are anti-nutritional compounds that accumulate in the cotyledons of faba beans. When humans consume beans with high levels of these compounds, it can cause a condition called favism in individuals harbouring a deficiency in the activity of their glucose-6-phosphate dehydrogenase. When faba beans are used in animal feeds, there can be effects on performance. These concerns have resulted in increasing interest within plant breeding in developing low vicine and convicine faba bean germplasm. In order to facilitate this objective, we developed a rapid and robust screening method for vicine and convicine, capable of distinguishing between faba beans that are either high (wild type) or low in vicine and convicine. In the absence of reliable commercial reference materials, we report an adaptation of a previously published method where a biochemical assay and spectral data were used to confirm the identity of our analytes, vicine and convicine. This method could be readily adopted in other facilities and open the way to the efficient exploitation of diverse germplasm in regions where faba beans play a significant role in human nutrition. We screened a collection of germplasm of interest to a collaborative plant breeding programme developing between the National Institute for Agricultural Botany in the UK and LInstitut Nationale dAgronomie de Tunisie in Tunisia. We report the results obtained and discuss the prospects for developing molecular markers for the low vicine and convicine trait.

Flanking SNP markers for vicine–convicine concentration in faba bean (Vicia faba L.)

The pyrimidine glycosides, vicine and convicine, limit the use of faba bean (Vicia faba L.) as food and feed. A single recessive gene, vc-, is responsible for a lowered vicine–convicine concentration. The biosynthetic pathway of these closely related compounds is not known, and the nearest available markers are several cM away from vc-. Improved markers would assist breeding and help to identify candidate genes. A segregating population of 210 F5 recombinant inbred lines was developed from the cross of Mélodie/2 (low vicine–convicine)xa0×xa0ILB 938/2 (normal vicine–convicine), and vicine–convicine concentrations were determined twice on each line. The population was genotyped with a set of 188 SNPs. A strong, single QTL for vicine–convicine concentration was identified on chromosome I, flanked by markers 1.0xa0cM away on one side and 2.6xa0cM on the other. The interval defined by these markers in the model species Medicago truncatula includes about 340 genes, but no candidate genes were identified. Further fine mapping should lead to the identification of tightly linked markers as well as narrowing down the search for candidate regulatory or biosynthetic genes which could underlie the vc- locus.