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Öğe Amino acid and fatty acid profiles of perennial Baki™ bean(Frontiers Media Sa, 2024) Craine, Evan B.; Barriball, Spencer; Sakiroglu, Muhammet; Peters, Tessa; Schlautman, BrandonTo realize the potential of sainfoins to contribute to sustainable agriculture and expand on demonstrated uses and benefits, de novo domestication is occurring to develop perennial Baki (TM) bean, the trade name used by The Land Institute for pulses (i.e., grain legumes) derived from sainfoins. The objective of this study was to characterize amino acid and fatty acid profiles of depodded seeds from commercial sainfoin (Onobrychis viciifolia) seed lots, and compare these results with data published in the Global Food Composition Database for Pulses. The fatty acid profile consisted primarily of polyunsaturated fatty acids (56.8%), compared to monounsaturated (29.0%) and saturated fatty acids (14.2%), and n-3 fatty acids (39.5%), compared to n-9 (28.4%) and n-6 (17.6%) fatty acids. The essential fatty acid linolenic acid (18,3 n-3) was the most abundant fatty acid (39.2%), followed by oleic acid (18,1 cis-9) (27.8%), and the essential fatty acid linoleic acid (18,2 n-6) (17.3%). The amino acid profile consisted primarily of the nonessential amino acids glutamic acid (18.3%), arginine (11.6%), and aspartic acid (10.8%), followed by the essential amino acids leucine (6.8%), and lysine (5.8%). Essential amino acid content met adult daily requirements for each amino acid. This indicates that sainfoin seeds may be a complete plant protein source. However, further research is necessary to better understand protein quality, defined by protein digestibility in addition to the amino acid profile. By demonstrating favorable fatty acid and amino acid profiles to human health, these results contribute to a growing body of evidence supporting the potential benefits of perennial Baki (TM) bean, a novel, perennial pulse derived from sainfoins.Öğe Annual and perennial Medicago show signatures of parallel adaptation to climate and soil in highly conserved genes(Wiley, 2021) Blanco-Pastor, Jose Luis; Liberal, Isabel M.; Sakiroglu, Muhammet; Wei, Yanling; Brummer, E. Charles; Andrew, Rose L.; Pfeil, Bernard E.Human induced environmental change may require rapid adaptation of plant populations and crops, but the genomic basis of environmental adaptation remain poorly understood. We analysed polymorphic loci from the perennial crop Medicago sativa (alfalfa or lucerne) and the annual legume model species M. truncatula to search for a common set of candidate genes that might contribute to adaptation to abiotic stress in both annual and perennial Medicago species. We identified a set of candidate genes of adaptation associated with environmental gradients along the distribution of the two Medicago species. Candidate genes for each species were detected in homologous genomic linkage blocks using genome-environment (GEA) and genome-phenotype association analyses. Hundreds of GEA candidate genes were species-specific, of these, 13.4% (M. sativa) and 24% (M. truncatula) were also significantly associated with phenotypic traits. A set of 168 GEA candidates were shared by both species, which was 25.4% more than expected by chance. When combined, they explained a high proportion of variance for certain phenotypic traits associated with adaptation. Genes with highly conserved functions dominated among the shared candidates and were enriched in gene ontology terms that have shown to play a central role in drought avoidance and tolerance mechanisms by means of cellular shape modifications and other functions associated with cell homeostasis. Our results point to the existence of a molecular basis of adaptation to abiotic stress in Medicago determined by highly conserved genes and gene functions. We discuss these results in light of the recently proposed omnigenic model of complex traits.Öğe Annual and perennial Medicago show signatures of parallel adaptation to climate and soil in highly conserved genes(Wiley, 2021) Blanco-Pastor, Jose Luis; Liberal, Isabel M.; Sakiroglu, Muhammet; Wei, Yanling; Brummer, E. Charles; Andrew, Rose L.; Pfeil, Bernard E.Human induced environmental change may require rapid adaptation of plant populations and crops, but the genomic basis of environmental adaptation remain poorly understood. We analysed polymorphic loci from the perennial crop Medicago sativa (alfalfa or lucerne) and the annual legume model species M. truncatula to search for a common set of candidate genes that might contribute to adaptation to abiotic stress in both annual and perennial Medicago species. We identified a set of candidate genes of adaptation associated with environmental gradients along the distribution of the two Medicago species. Candidate genes for each species were detected in homologous genomic linkage blocks using genome-environment (GEA) and genome-phenotype association analyses. Hundreds of GEA candidate genes were species-specific, of these, 13.4% (M. sativa) and 24% (M. truncatula) were also significantly associated with phenotypic traits. A set of 168 GEA candidates were shared by both species, which was 25.4% more than expected by chance. When combined, they explained a high proportion of variance for certain phenotypic traits associated with adaptation. Genes with highly conserved functions dominated among the shared candidates and were enriched in gene ontology terms that have shown to play a central role in drought avoidance and tolerance mechanisms by means of cellular shape modifications and other functions associated with cell homeostasis. Our results point to the existence of a molecular basis of adaptation to abiotic stress in Medicago determined by highly conserved genes and gene functions. We discuss these results in light of the recently proposed omnigenic model of complex traits.Öğe Evaluating macro- and micro-mineral contents and agronomic traits of Turkish oat landraces(Wiley, 2022) Kilinc, Fatih Mehmet; Sakiroglu, Muhammet; Yilmaz, Cafer Hakan; Akkaya, Aydin; Dokuyucu, Tevrican; Gezginc, Hasan; Yuce, IlkerThe cultivated oat (Avena sativa L. and A. byzantina Coch.) is an important annual cereal and forage plant. A large collection of historical oat landraces gathered from different diversity centers is maintained in various seed banks. A historical oat collection consisted of 174 Turkish landraces were evaluated for agronomic performance and mineral nutrient content. The experiment was arranged in an augmented design with six replications of 10 check cultivars and 29 landraces in each block. The most important finding of the study was that the landraces manifested a wide range of variation in all agronomic traits and that some historical landraces outperformed the check cultivars. Since it was dry for the grain-filling period (GFP) in 2019, some drought-tolerant landraces were identified. In addition, the top 10 landraces for yield and mineral content were also identified based on each year's performance as well as on the 3-yr average. The landrace TL69/PI411401 was found to be prominent for high calcium (Ca), magnesium (Mg), phosphorus (P), boron (B), and zinc (Zn) content; TL86/PI167378 for Ca, P, potassium (K), and iron (Fe) contents; and TL71/PI411414 for Ca, P, B, and Zn content.Öğe How does nitrogen and forage harvest affect belowground biomass and nonstructural carbohydrates in dual-use Kernza intermediate wheatgrass?(John Wiley and Sons Inc, 2020) Sakiroglu, Muhammet; Dong, Chenfei; Hall, Mary Beth; Jungers, Jacob; Picasso, ValentinIntermediate wheatgrass [Thinopyrum intermedium (Host) Barkworth & D.R. Dewey] is a cool-season perennial forage grass, whose grain is commercialized in the United States as “Kernza.” Its extensive root system may help in reducing soil erosion, water pollution, and C emissions. Nitrogen fertilization and forage harvest intensity may affect the belowground biomass and nonstructural carbohydrate (NSC) concentrations, which may affect growth in subsequent years. We compared N doses and forage harvest treatments in a replicated complete block experiment in three environments (location-years: Arlington, WI, 2016 and 2017; and St. Paul, MN, 2016). Seeds were sown in the fall, Kernza grain was harvested in the following summer, and rhizomes and roots were sampled in fall to a depth of 0.1 m over 2 yr. The water-soluble carbohydrates (WSC) accounted for 97–99% of NSC, across environments. The WSC concentration was higher in rhizomes than in roots in both years, but WSC mass was higher in roots than rhizomes due to greater root biomass. Nitrogen generally did not change NSC concentrations across years, but reduced WSC in rhizome the second year in WI. Forage harvest did not affect NSC concentrations across locations and years. Belowground biomass to 1-m depth in the fall of the second year in Wisconsin averaged 478.3 g m?2 regardless of treatment. Summer forage yield in the following year was positively associated with root biomass in the fall. These results suggest that harvesting forage in a Kernza dual-use system is not detrimental to intermediate wheatgrass above- and belowground productivity. © 2020 The Authors. Crop Science published by Wiley Periodicals, Inc. on behalf of Crop Science Society of AmericaÖğe Medicago sativa species complex: Revisiting the century-old problem in the light of molecular tools(Wiley, 2021) Sakiroglu, Muhammet; Ilhan, DoganThe genus Medicago is an important component of legumes and includes the model legume barrel-clover (Medicago truncatula Gaertn.) and widely cultivated forage crop alfalfa (M. sativa L.). The complex taxonomic group known as the M. sativa species complex, or M. sativa-falcata species complex, includes a number of taxa along with cultivated alfalfa that naturally distributed throughout northern Eurasia. Largely because of the millennia-long economic importance, the taxa have been in the center of attention. In the context of the efforts to understand taxonomic units included in the complex, a wide range of tools have been exploited. The early tools available were morphological traits such as flower color, pod shape, and pollen shape. The large conflict and discrepancy among researchers regarding the statue of the taxa sourced from the fact that a few genes controlled each of the morphological traits used. Thus, the morphology-based classification was proved to be contradictory. As the molecular tools became available and the research intensified, the initial species status generously granted to the taxa was questioned, and all the taxa denoted as species earlier were relegated to subspecific level. We are aiming to provide an up-to-date comprehensive picture for the complex in the light of recent molecular studies.Öğe Nutritional quality of Onobrychis viciifolia (Scop.) seeds: A potentially novel perennial pulse crop for human use(Wiley, 2023) Craine, Evan B.; Sakiroglu, Muhammet; Peters, Tessa E.; Barriball, Spencer; Schlautman, BrandonOnobrychis viciifolia (hereafter sainfoin) is an autotetraploid (2n = 4x = 28), allogamous insect-pollinated perennial legume originating from the Caucasus that has historically been cultivated as a forage. As a perennial legume, sainfoin has the potential to improve the sustainability of agriculture and food systems in multiple ways. Sainfoin can provide continuous living cover and biological nitrogen fixation to enhance soil fertility and health. It can also provide ecosystem services as a resource for pollinators and wildlife in addition to nitrogen fixation. Building on this history of valuable uses, The Land Institute is developing sainfoin as a pulse crop for human use. With the goal of supporting human diets with a sustainable, perennial protein source and nutrient-dense crop, this innovation requires a thorough understanding of the chemical composition of sainfoin seeds to ensure safety and potential nutritional quality. Using seeds from commercial sainfoin varieties developed for forage production, grown by commercial sainfoin seed growers in the western United States, this study evaluates seed composition as part of an ongoing investigation into sainfoin's potential as a novel pulse. We found crude protein content (38.78%) comparable with soybean and lupine, fat content (6.96%) comparable with lupine and chickpea, and starch (7.1%) and dietary fiber content (48.96%) comparable with lupine. Phytic acid content was higher than pulses (1790.89 mg). Ash (3.81%), iron (64.14 ppm), and zinc contents (61.63 ppm) were in the higher end of the range for pulses. This study indicates that sainfoin could become a novel, nutrient-dense crop for human nutrition. Future studies are required to further characterize seed composition and safety and demonstrate how common legume processing techniques may influence nutritional quality.Öğe Perennial Baki™ Bean Safety for Human Consumption: Evidence from an Analysis of Heavy Metals, Folate, Canavanine, Mycotoxins, Microorganisms and Pesticides(Mdpi, 2024) Craine, Evan B.; Sakiroglu, Muhammet; Barriball, Spencer; Peters, Tessa E.; Schlautman, BrandonGlobal food production relies on annual grain crops. The reliability and productivity of these crops are threatened by adaptations to climate change and unsustainable rates of soil loss associated with their cultivation. Perennial grain crops, which do not require planting every year, have been proposed as a transformative solution to these challenges. Perennial grain crops typically rely on wild species as direct domesticates or as sources of perenniality in hybridization with annual grains. Onobrychis spp. (sainfoins) are a genus of perennial legumes domesticated as ancient forages. Baki (TM) bean is the tradename for pulses derived from sainfoins, with ongoing domestication underway to extend demonstrated benefits to sustainable agriculture. This study contributes to a growing body of evidence characterizing the nutritional quality of Baki (TM) bean. Through two studies, we investigated the safety of Baki (TM) bean for human consumption. We quantified heavy metals, folate, and canavanine for samples from commercial seed producers, and we quantified levels of mycotoxins, microorganisms, and pesticides in samples from a single year and seed producer, representing different varieties and production locations. The investigated analytes were not detectable or occurred at levels that do not pose a significant safety risk. Overall, this study supports the safety of Baki (TM) bean for human consumption as a novel pulse crop.Öğe The chromosome-level assembly of the wild diploid alfalfa genome provides insights into the full landscape of genomic variations between cultivated and wild alfalfa(Wiley, 2024) Shi, Kun; Dong, Hongbin; Du, Huilong; Li, Yuxian; Zhou, Le; Liang, Chengzhi; Sakiroglu, MuhammetAlfalfa (Medicago sativa L.) is one of the most important forage legumes in the world, including autotetraploid (M. sativa ssp. sativa) and diploid alfalfa (M. sativa ssp. caerulea, progenitor of autotetraploid alfalfa). Here, we reported a high-quality genome of ZW0012 (diploid alfalfa, 769 Mb, contig N50 = 5.5 Mb), which was grouped into the Northern group in population structure analysis, suggesting that our genome assembly filled a major gap among the members of M. sativa complex. During polyploidization, large phenotypic differences occurred between diploids and tetraploids, and the genetic information underlying its massive phenotypic variations remains largely unexplored. Extensive structural variations (SVs) were identified between ZW0012 and XinJiangDaYe (an autotetraploid alfalfa with released genome). We identified 71 ZW0012-specific PAV genes and 1296 XinJiangDaYe-specific PAV genes, mainly involved in defence response, cell growth, and photosynthesis. We have verified the positive roles of MsNCR1 (a XinJiangDaYe-specific PAV gene) in nodulation using an Agrobacterium rhizobia-mediated transgenic method. We also demonstrated that MsSKIP23_1 and MsFBL23_1 (two XinJiangDaYe-specific PAV genes) regulated leaf size by transient overexpression and virus-induced gene silencing analysis. Our study provides a high-quality reference genome of an important diploid alfalfa germplasm and a valuable resource of variation landscape between diploid and autotetraploid, which will facilitate the functional gene discovery and molecular-based breeding for the cultivars in the future.Öğe The chromosome-level assembly of the wild diploid alfalfa genome provides insights into the full landscape of genomic variations between cultivated and wild alfalfa(Wiley, 2024) Shi, Kun; Dong, Hongbin; Du, Huilong; Li, Yuxian; Zhou, Le; Liang, Chengzhi; Sakiroglu, MuhammetAlfalfa (Medicago sativa L.) is one of the most important forage legumes in the world, including autotetraploid (M. sativa ssp. sativa) and diploid alfalfa (M. sativa ssp. caerulea, progenitor of autotetraploid alfalfa). Here, we reported a high-quality genome of ZW0012 (diploid alfalfa, 769 Mb, contig N50 = 5.5 Mb), which was grouped into the Northern group in population structure analysis, suggesting that our genome assembly filled a major gap among the members of M. sativa complex. During polyploidization, large phenotypic differences occurred between diploids and tetraploids, and the genetic information underlying its massive phenotypic variations remains largely unexplored. Extensive structural variations (SVs) were identified between ZW0012 and XinJiangDaYe (an autotetraploid alfalfa with released genome). We identified 71 ZW0012-specific PAV genes and 1296 XinJiangDaYe-specific PAV genes, mainly involved in defence response, cell growth, and photosynthesis. We have verified the positive roles of MsNCR1 (a XinJiangDaYe-specific PAV gene) in nodulation using an Agrobacterium rhizobia-mediated transgenic method. We also demonstrated that MsSKIP23_1 and MsFBL23_1 (two XinJiangDaYe-specific PAV genes) regulated leaf size by transient overexpression and virus-induced gene silencing analysis. Our study provides a high-quality reference genome of an important diploid alfalfa germplasm and a valuable resource of variation landscape between diploid and autotetraploid, which will facilitate the functional gene discovery and molecular-based breeding for the cultivars in the future.
