Protein content and HvNAM alleles in Nordic barley (Hordeum vulgare) during a century of breeding.

BACKGROUND: Barley has been bred for more than a century in the Nordic countries, with dramatic improvements of yield traits. In this study we investigate if this has come at the cost of lower grain protein and micronutrient (iron, zinc) content, by analysing 80 accessions representing four different improvement stages. We further re-sequenced the two grain protein content associated genes HvNAM-1 and HvNAM-2 in full and performed expression analyses of the same genes to search for genetic associations with nutrient content. RESULTS: We found higher thousand grain weight in barley landraces and in accessions from the late improvement group compared to accessions from the mid of the twentieth century. Straw length was much reduced in late stage accessions. No significant temporal decrease in grain protein, iron or zinc content during twentieth century Nordic crop improvement could be detected. Out of the 80 accessions only two deviant HvNAM-1 sequences were found, represented by one accession each. These do not appear to be correlated to grain protein content. The sequence of HvNAM-2 was invariable in all accessions and no correlations between expression levels of HvNAM-1 and HvNAM-2 and with grain protein content was found. CONCLUSIONS: In contrast to studies in wheat, where a strong negative correlation between straw length and grain protein and micronutrient content has been found, we do not see this relationship in Nordic barley. The last 60 years of breeding has reduced straw length but, contrary to expectations, not protein and micronutrient content. Variation in grain protein and micronutrient content was found among the Nordic barley accessions, but it is not explained by variation of HvNAM genes. This means that HvNAM is an unexploited source of genetic variation for nutrient content in Nordic barley.

Population structure in landrace barley (Hordeum vulgare L.) during the late 19th century crop failures in Fennoscandia.

Agricultural disasters and the subsequent need for supply of relief seed can be expected to influence the genetic composition of crop plant populations. The consequences of disasters and seed relief have, however, rarely been studied since specimens sampled before the events are seldomly available. A series of crop failures struck northern Fennoscandia (Norway, Sweden and Finland) during the second half of the 19th century. In order to assess population genetic dynamics of landrace barley (Hordeum vulgare), and consequences of crop failure and possible seed relief during this time period, we genotyped seeds from 16 historical accessions originating from two time periods spanning the period of repeated crop failure. Reliable identification of genetic structuring is highly dependent on sampling regimes and detecting fine-scale geographic or temporal differentiation requires large sample sizes. The robustness of the results under different sampling regimes was evaluated by analyzing subsets of the data and an artificially pooled dataset. The results led to the conclusion that six individuals per accession were insufficient for reliable detection of the observed genetic structure. We found that population structure among the data was best explained by collection year of accessions, rather than geographic origin. The correlation with collection year indicated a change in genetic composition of landrace barley in the area after repeated crop failures, likely a consequence of introgression of relief seed in local populations. Identical genotypes were found to be shared among some accessions, suggesting founder effects and local seed exchange along known routes for trade and cultural exchange.

Patterns of Exchange of Multiplying Onion (Allium cepa L. Aggregatum-Group) in Fennoscandian Home Gardens.

Multiplying onion (Allium cepa L. Aggregatum-Group), commonly known as shallot or potato onion, has a long tradition of cultivation in Fennoscandian home gardens. During the last decades, more than 80 accessions, maintained as vegetatively propagated clones, have been gathered from home gardens in all Fennoscandian countries. A genetic analysis showed regional patterns of accessions belonging to the same genetic group. However, accessions belonging to the same genetic group could originate in any of the countries. These results suggested both short- and long-distance exchange of set onions, which was confirmed by several survey responses. Some of the most common genetic groups also resembled different modern varieties. The morphological characterization illustrated that most characters were strongly influenced by environment and set onion properties. The only reliably scorable trait was bulb skin color. Neither our morphological nor genetic results support a division between potato onions and shallots. Instead, naming seems to follow linguistic traditions. An ethnobotanical survey tells of the Fennoscandian multiplying onions as being a crop with reliable harvest, excellent storage ability, and good taste. An increased cultivation of this material on both household and commercial scale should be possible.

Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat.

BACKGROUND: The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on senescence rate and grain size. First detected in wild emmer wheat, the wild-type allele of the gene has been introgressed into durum and bread wheat. Later studies have, however, also found the presence of the wild-type allele in some domesticated subspecies. In this study we trace the evolutionary history of the NAM-B1 in tetraploid wheat species and evaluate it as a putative domestication gene. RESULTS: Genotyping of wild and landrace tetraploid accessions showed presence of only null alleles in durum. Domesticated emmer wheats contained both null alleles and the wild-type allele while wild emmers, with one exception, only carried the wild-type allele. One of the null alleles consists of a deletion that covers several 100 kb. The other null-allele, a one-basepair frame-shift insertion, likely arose among wild emmer. This allele was the target of a selective sweep, extending over several 100 kb. CONCLUSIONS: The NAM-B1 gene fulfils some criteria for being a domestication gene by encoding a trait of domestication relevance (seed size) and is here shown to have been under positive selection. The presence of both wild-type and null alleles in domesticated emmer does, however, suggest the gene to be a diversification gene in this species. Further studies of genotype-environment interactions are needed to find out under what conditions selection on different NAM-B1 alleles have been beneficial.

Geographical distribution of genetic diversity in Secale landrace and wild accessions.

BACKGROUND: Rye, Secale cereale L., has historically been a crop of major importance and is still a key cereal in many parts of Europe. Single populations of cultivated rye have been shown to capture a large proportion of the genetic diversity present in the species, but the distribution of genetic diversity in subspecies and across geographical areas is largely unknown. Here we explore the structure of genetic diversity in landrace rye and relate it to that of wild and feral relatives. RESULTS: A total of 567 SNPs were analysed in 434 individuals from 76 accessions of wild, feral and cultivated rye. Genetic diversity was highest in cultivated rye, slightly lower in feral rye taxa and significantly lower in the wild S. strictum Presl. and S. africanum Stapf. Evaluation of effects from ascertainment bias suggests underestimation of diversity primarily in S. strictum and S. africanum. Levels of ascertainment bias, STRUCTURE and principal component analyses all supported the proposed classification of S. africanum and S. strictum as a separate species from S. cereale. S. afghanicum (Vav.) Roshev, S. ancestrale Zhuk., S. dighoricum (Vav.) Roshev, S. segetale (Zhuk.) Roshev and S. vavilovii Grossh. seemed, in contrast, to share the same gene pool as S. cereale and their genetic clustering was more dependent on geographical origin than taxonomic classification. S. vavilovii was found to be the most likely wild ancestor of cultivated rye. Among cultivated rye landraces from Europe, Asia and North Africa five geographically discrete genetic clusters were identified. These had only limited overlap with major agro-climatic zones. Slash-and-burn rye from the Finnmark area in Scandinavia formed a distinct cluster with little similarity to other landrace ryes. Regional studies of Northern and South-West Europe demonstrate different genetic distribution patterns as a result of varying cultivation intensity. CONCLUSIONS: With the exception of S. strictum and S. africanum different rye taxa share the majority of the genetic variation. Due to the vast sharing of genetic diversity within the S. cereale clade, ascertainment bias seems to be a lesser problem in rye than in predominantly selfing species. By exploiting within accession diversity geographic structure can be shown on a much finer scale than previously reported.

Flowering time adaption in Swedish landrace pea (Pisum sativum L.).

BACKGROUND: Cultivated crops have repeatedly faced new climatic conditions while spreading from their site of origin. In Sweden, at the northernmost fringe of Europe, extreme conditions with temperature-limited growth seasons and long days require specific adaptation. Pea (Pisum sativum L.) has been cultivated in Sweden for millennia, allowing for adaptation to the local environmental conditions to develop. To study such adaptation, 15 Swedish pea landraces were chosen alongside nine European landraces, seven cultivars and three wild accessions. Number of days to flowering (DTF) and other traits were measured and the diversity of the flowering time genes HIGH RESPONSE TO PHOTOPERIOD (HR), LATE FLOWERING (LF) and STERILE NODES (SN) was assessed. Furthermore, the expression profiles of LF and SN were obtained. RESULTS: DTF was positively correlated with the length of growing season at the site of origin (GSO) of the Swedish landraces. Alleles at the HR locus were significantly associated with DTF with an average difference of 15.43 days between the two detected haplotypes. LF expression was found to have a significant effect on DTF when analysed on its own, but not when HR haplotype was added to the model. HR haplotype and GSO together explained the most of the detected variation in DTF (49.6 %). CONCLUSIONS: We show local adaptation of DTF, primarily in the northernmost accessions, and links between genetic diversity and diversity in DTF. The links between GSO and genetic diversity of the genes are less clear-cut and flowering time adaptation seems to have a complex genetic background.

Wheat in the Mediterranean revisited--tetraploid wheat landraces assessed with elite bread wheat Single Nucleotide Polymorphism markers.

BACKGROUND: Single Nucleotide Polymorphism (SNP) panels recently developed for the assessment of genetic diversity in wheat are primarily based on elite varieties, mostly those of bread wheat. The usefulness of such SNP panels for studying wheat evolution and domestication has not yet been fully explored and ascertainment bias issues can potentially affect their applicability when studying landraces and tetraploid ancestors of bread wheat. We here evaluate whether population structure and evolutionary history can be assessed in tetraploid landrace wheats using SNP markers previously developed for the analysis of elite cultivars of hexaploid wheat. RESULTS: We genotyped more than 100 tetraploid wheat landraces and wild emmer wheat accessions, some of which had previously been screened with SSR markers, for an existing SNP panel and obtained publically available genotypes for the same SNPs for hexaploid wheat varieties and landraces. Results showed that quantification of genetic diversity can be affected by ascertainment bias but that the effects of ascertainment bias can at least partly be alleviated by merging SNPs to haplotypes. Analyses of population structure and genetic differentiation show strong subdivision between the tetraploid wheat subspecies, except for durum and rivet that are not separable. A more detailed population structure of durum landraces could be obtained than with SSR markers. The results also suggest an emmer, rather than durum, ancestry of bread wheat and with gene flow from wild emmer. CONCLUSIONS: SNP markers developed for elite cultivars show great potential for inferring population structure and can address evolutionary questions in landrace wheat. Issues of marker genome specificity and mapping need, however, to be addressed. Ascertainment bias does not seem to interfere with the ability of a SNP marker system developed for elite bread wheat accessions to detect population structure in other types of wheat.

Strong presence of the high grain protein content allele of NAM-B1 in Fennoscandian wheat.

Grain protein content in wheat has been shown to be affected by the NAM-B1 gene where the wildtype allele confers high levels of protein and micronutrients but can reduce yield. Two known non-functional alleles instead increase yield but lead to lower levels of protein and micronutrients. The wildtype allele in hexaploid bread wheat is so far mainly known from historical specimens and a few lines with an emmer wheat introgression. Here we report a screening for the wildtype allele in wheats of different origin. First, a worldwide core collection of 367 bread wheats with worldwide origin was screened and five accessions carrying the wildtype NAM-B1 allele were found. Several of these could be traced to a Fennoscandian origin and the wildtype allele was more frequent in spring wheat. These findings, together with the late maturation of spring wheat, suggested that the faster maturation caused by the wildtype allele might have preserved it in areas with a short growing season. Thus a second set consisting of 138 spring wheats of a northern origin was screened and as many as 33 % of the accessions had the wildtype allele, all of a Fennoscandian origin. The presence of the wildtype allele in landraces and cultivars is in agreement with the use of landraces in Fennoscandian wheat breeding. Last, 22 spelt wheats, a wheat type previously suggested to carry the wildtype allele, were screened and five wildtype accessions found. The wildtype NAM-B1 accessions found could be a suitable material for plant breeding efforts directed towards increasing the nutrient content of bread wheat.

Allelic variation at the Rht8 locus in a 19th century wheat collection.

Wheat breeding during the 20th century has put large efforts into reducing straw length and increasing harvest index. In the 1920s an allele of Rht8 with dwarfing effects, found in the Japanese cultivar "Akakomugi," was bred into European cultivars and subsequently spread over the world. Rht8 has not been cloned, but the microsatellite marker WMS261 has been shown to be closely linked to it and is commonly used for genotyping Rht8. The "Akakomugi" allele is strongly associated with WMS261-192bp. Numerous screens of wheat cultivars with different geographical origin have been performed to study the spread and influence of the WMS261-192bp during 20th century plant breeding. However, the allelic diversity of WMS261 in wheat cultivars before modern plant breeding and introduction of the Japanese dwarfing genes is largely unknown. Here, we report a study of WMS261 allelic diversity in a historical wheat collection from 1865 representing worldwide major wheats at the time. The majority carried the previously reported 164 bp or 174 bp allele, but with little geographical correlation. In a few lines, a rare 182 bp fragment was found. Although straw length was recognized as an important character already in the 19th century, Rht8 probably played a minor role for height variation. The use of WMS261 and other functional markers for analyses of historical specimens and characterization of historic crop traits is discussed.

Nineteenth century seeds reveal the population genetics of landrace barley (Hordeum vulgare).

Barley (Hordeum vulgare) is a major crop, grown worldwide and in a wide range of climatic conditions. Despite its importance as a crop species, little is known about the population genetics of barley and the effects of bottlenecks, adaptation, and gene flow on genetic diversity within and between landrace populations. In areas with highly developed agriculture, such as Northern Europe, these types of genetic studies are hampered by lack of landraces preserved in situ or ex situ. Here, we report a genetic study of Swedish landrace barley using 113-year-old seed samples. The results demonstrate differing levels of variation with some latitudinal effect. We also detect clear population differentiation and population structure within Sweden into a southern and a northern cluster. These results possibly reflect different introduction routes of barley into Sweden. We thus show that the study of historic material can be an important alternative for regions where no or little extant landrace material is available.

Trait Expression and Environmental Responses of Pea (Pisum sativum L.) Genetic Resources Targeting Cultivation in the Arctic.

In the Arctic part of the Nordic region, cultivated crops need to specifically adapt to adverse and extreme climate conditions, such as low temperatures, long days, and a short growing season. Under the projected climate change scenarios, higher temperatures and an earlier spring thaw will gradually allow the cultivation of plants that could not be previously cultivated there. For millennia, Pea (Pisum sativum L.) has been a major cultivated protein plant in Nordic countries but is currently limited to the southern parts of the region. However, response and adaptation to the Arctic day length/light spectrum and temperatures are essential for the productivity of the pea germplasm and need to be better understood. This study investigated these factors and identified suitable pea genetic resources for future cultivation and breeding in the Arctic region. Fifty gene bank accessions of peas with a Nordic landrace or cultivar origin were evaluated in 2-year field trials at four Nordic locations in Denmark, Finland, Sweden, and Norway (55° to 69° N). The contrasting environmental conditions of the trial sites revealed differences in expression of phenological, morphological, crop productivity, and quality traits in the accessions. The data showed that light conditions related to a very long photoperiod partly compensated for the lack of accumulated temperature in the far north. A critical factor for cultivation in the Arctic is the use of cultivars with rapid flowering and maturation times combined with early sowing. At the most extreme site (69°N), no accession reached full maturation. Nonetheless several accessions, predominantly landraces of a northern origin, reached a green harvest state. All the cultivars reached full maturation at the sub-Arctic latitude in northern Sweden (63°N) when plants were established early in the season. Seed yield correlated positively with seed number and aboveground biomass, but negatively with flowering time. A high yield potential and protein concentration of dry seed were found in many garden types of pea, confirming their breeding potential for yield. Overall, the results indicated that pea genetic resources are available for breeding or immediate cultivation, thus aiding in the northward expansion of pea cultivation. Predicted climate changes would support this expansion.

Crop and Livestock Diversity Cultivating Gastronomic Potential, Illustrated by Sensory Profiles of Landraces.

Landraces, that is, crop and livestock not improved by formal breeding, are scarce in the industrialized world and are mainly maintained ex situ for breeding purposes. The natural biodiversity of these landraces may contribute to securing food production that can adapt to a changing climate, crop pathogens, diseases, and other agricultural challenges. In addition, landraces might also possess unique quality traits. Our aim is to take the idea of crop and livestock diversity further by connecting flavor differences of different landraces and varieties, with gastronomic applications. Do landraces provide a creative possibility of using distinct sensory characteristics to create new dishes and food products and/or to optimize recipes by finding the right variety for existing dishes and food products? This study suggests that apple, pea, pear, and poultry landraces, apart from being valuable in terms of biodiversity in sustainable food systems, also possess unique and distinct gastronomic potential. For example, citrus odors in apples, nutty taste in gray peas, astringent taste in pears, and high odor intensity of stable in poultry is of culinary relevance when working with apple juice, plant-based alternatives to meat, poached pears, and roasted rooster, respectively. To fully explore, and take advantage of, the gastronomic potential landraces possess, additional studies are needed in order to find suitable cooking methods and development of recipes. PRACTICAL APPLICATION: Seeking to increase market interest for landraces, highlighting gastronomic values could stimulate higher demand and, in turn, contribute to larger and more resilient populations preserved in situ. Specifically, the paper is of use to (I) crop and livestock producers and food companies who wish to provide products with greater sensory variation, (II) individuals, companies, and organizations with the aim to increase landrace demand and/or preservation, and (III) breeders and genetic engineers managing genetic traits of landraces and other varieties.

Swedish spring wheat varieties with the rare high grain protein allele of NAM-B1 differ in leaf senescence and grain mineral content.

Some Swedish spring wheat varieties have recently been shown to carry a rare wildtype (wt) allele of the gene NAM-B1, known to affect leaf senescence and nutrient retranslocation to the grain. The wt allele is believed to increase grain protein concentration and has attracted interest from breeders since it could contribute to higher grain quality and more nitrogen-efficient varieties. This study investigated whether Swedish varieties with the wt allele differ from varieties with one of the more common, non-functional alleles in order to examine the effect of the gene in a wide genetic background, and possibly explain why the allele has been retained in Swedish varieties. Forty varieties of spring wheat differing in NAM-B1 allele type were cultivated under controlled conditions. Senescence was monitored and grains were harvested and analyzed for mineral nutrient concentration. Varieties with the wt allele reached anthesis earlier and completed senescence faster than varieties with the non-functional allele. The wt varieties also had more ears, lighter grains and higher yields of P and K. Contrary to previous information on effects of the wt allele, our wt varieties did not have increased grain N concentration or grain N yield. In addition, temporal studies showed that straw length has decreased but grain N yield has remained unaffected over a century of Swedish spring wheat breeding. The faster development of wt varieties supports the hypothesis of NAM-B1 being preserved in Fennoscandia, with its short growing season, because of accelerated development conferred by the NAM-B1 wt allele. Although the possible effects of other gene actions were impossible to distinguish, the genetic resource of Fennoscandian spring wheats with the wt NAM-B1 allele is interesting to investigate further for breeding purposes.