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Seed dormancy is an important breeding trait for the development of certain types of peanut cultivars. Peanut cultivars with seed dormancy can inhibit preharvest sprouting in which the sprouting may increase susceptibility to preharvest aflatoxin contamination. The recombinant inbred line (RIL) mapping population derived from a cross of Tifrunner, a dormant Runner type, and GT-C20, a non-dormant Spanish type, were planted in the field for 2 years, and the freshly harvested seeds were used for seed dormancy tests at 7, 14, 21, and 28 days during germination. There were three RILs from 2-year tests with no dormancy (T48, T83, T160) and two lines with strong dormancy (T11, T163). This RIL population was genotyped using peanut SNP array ‘Axiom_Arachis’ 58 K, and two major seed dormancy QTLs were anchored on chromosome A04 and A05 with 43.16% and 51.61% of the phenotype variation explained (PVE), respectively. The QTL mapped on chromosome A05 had been anchored on a physical map interval of 98 kb (157.538–157.636 Mb) from which a possible candidate gene (Arahy.KB746A, ethylene-responsive transcription factor) was identified. Reference to the peanut physical map and flanking sequences, DNA markers can be developed for these two QTLs and used in marker-assisted breeding selection for seed dormancy in peanut.

Seeds kept in long-term storage are essential for maintaining genetic resources of crops and other plant materials in seed banks and national germplasm systems. But seeds undergo chemical changes over time as part of the ageing process that result in reduced germination rates and seedling normalcy. For example, oilseed crops such as peanuts are particularly vulnerable to oxidation and rancidification due to their high oil content. To test the effect of storage time on seed oil in peanuts, we grew different accessions and harvested fresh seeds to compare the oil composition of new seeds with seeds aged in storage for varying lengths of time. Out of the nine fatty acids detected and measured by gas chromatography, five including oleic, gadoleic, behenic, lignoceric and cerotic acids differed significantly between new and old seeds. Additionally, old seeds accumulated up to four oxidation products together averaging about 1% of the total oil composition. The concentration of these oxidation products was positively correlated with the age of the seeds, increasing linearly up to more than 6% of the total in the oldest seeds. The presence and concentration of oxidation products measured using simple chromatography techniques can be used as an initial indication of quality and viability in older seed inventories stored in germplasm repositories.

Introduction Ovine interferon-tau (oIFN-τ) is a newly discovered type I interferon. This study used biochemical techniques to transform the oIFN-τ gene into Escherichia coli to obtain the mass and soluble expression of the recombinant protein. Material and Methods First, total RNA was extracted from fresh sheep embryonic tissues with TRIzol reagent and then used as a template to reverse transcribe and amplify the mature oIFN-τ gene with RT-PCR. The amplified product was next digested with the HindIII and XhoI restriction enzymes and inserted into the pET-32a(+) vector to construct the prokaryotic expression plasmid. The corrected in-frame recombinant plasmid, pET-32a(+)-oIFN-τ, was transformed into E. coli Rosetta (DE3) competent cells. After induction with isopropyl-beta-D-thiogalactopyranoside (IPTG), the recombinant protein was detected in bacteria. Finally, the bacteria were lysed by sonication, and the recombinant protein was purified by nickel affinity chromatography and DEAE anion exchange chromatography. Results The protein was confirmed to be oIFN-τ, which mainly existed in the soluble lysate fraction, as proven by SDS-PAGE and Western blot assays. Conclusion Purified IFN-τ exists mostly in a soluble form, and its anti-vesicular stomatitis virus (VSV) activity reached 7.08×10(6)IU/mL.

Among major cereals domesticated as staple food, only sorghum has a high proportion of cultivars with condensed tannins in grain, which can trigger bitter taste perception in animals by binding to type 2 taste receptors (TAS2Rs). Here, we report the completion of uncovering of a pair of duplicate recessive genes (Tannin1 and Tannin2) underlying tannin presence. Three loss-of-function alleles from each gene were identified in non-tannin sorghum desired as palatable food. Condensed tannins effectively prevented sparrows from consuming sorghum grain. Parallel geographic distributions between tannin sorghum and Quelea quelea supported the role of tannins in fighting against this major herbivore threat. Association between geographic distributions of human TAS2R variants and tannin sorghum across Africa suggested that different causes had probably driven this bidirectional selection according to varied local herbivore threats and human taste sensitivity. Our investigation uncovered coevolution among humans, plants and environments linked by allelochemicals.

Peanut is an important legume providing products with nutrient dense including mineral nutrition. However, the genetic basis underlying the variations in the mineral composition in peanut is still unknown. Genome-wide association studies (GWAS) of the concentrations of 13 mineral elements combined with coexpression network were performed using a diverse panel of 120 genotypes mainly selected from the U.S. peanut mini core collection. A total of 36 significant quantitative trait loci (QTLs) associated with five elemental concentrations were identified with phenotypic variation explained (PVE) from 18.35% to 27.56%, in which 24 QTLs were for boron (B), 2 QTLs for copper (Cu), 6 QTLs for sodium (Na), 3 QTLs for sulfur (S), and 1 QTL for zinc (Zn). A total of 110 nonredundant candidate causal genes identified were significantly associated with elemental accumulation, which included one high-priority overlap (HPO) candidate gene arahy.KQD4NT, an important elemental/metal transporter gene located on LGB04 with position 5,413,913-5,417,353.

Background Drugs that promote angiogenesis include statins, recombinant human granulocyte colony-stimulating factor, and stromal cell-derived factor-1. Low doses of atorvastatin could significantly increase the vascular expressions of endothelial growth factor, and the number of peripheral blood endothelial progenitor cells (EPCs), thus improving angiogenesis and local blood flow. G-CSF is an EPC-mobilization agent used in ischemia studies for targeting angiogenesis after cerebral ischemia via EPCs. In previous clinical trials, consistent conclusions have not been reached about the effectiveness of G-CSF on ischemic stroke. Therefore, the therapeutic effect of G-CSF and its combination with other medicines need further experimental verification. It is known that atorvastatin, rhG-CSF, and SDF-1 are considered the most promising neuroprotective candidates, but a comprehensive comparison of their effects is lacking. Aims To compare the effects of atorvastatin, stromal cell-derived factor-1, and recombinant human granulocyte colony-stimulating factor on ischemic stroke. Methods Adult male Sprague-Dawley rats were randomly allocated to three groups: normal, sham-operated, and middle cerebral artery occlusion operated. Middle cerebral artery occlusion operated rats were further allocated into saline, atorvastatin, recombinant human granulocyte colony-stimulating factor, and recombinant human granulocyte colony-stimulating factor + stromal cell-derived factor-1 groups. Neurological function evaluation, cerebral infarction and the blood–brain barrier integrity analysis, identification of angiogenic factors, assessment of angiogenesis, expression of growth-associated protein-43, neuroglobin, glial cell-derived neurotrophic factor, and cleaved caspase 3, were performed. Results Compared with atorvastatin or recombinant human granulocyte colony-stimulating factor alone, recombinant human granulocyte colony-stimulating factor + stromal cell-derived factor-1 treatment improved neurological performance, reduced cerebral infarction and blood–brain barrier disruption after stroke, and increased the content of stromal cell-derived factor-1, vascular endothelial growth factor, monocyte chemotactic protein 1, and basic fibroblast growth factor in peripheral blood. In addition, recombinant human granulocyte colony-stimulating factor + stromal cell-derived factor-1 promoted greater angiogenesis than atorvastatin or recombinant human granulocyte colony-stimulating factor alone and increased the expression of growth-associated protein-43, neuroglobin, and glial cell-derived neurotrophic factor, while decreasing the levels of cleaved caspase 3 in the brain after ischemic stroke. Conclusions Combination therapy with recombinant human granulocyte colony-stimulating factor and stromal cell-derived factor-1 is more effective than atorvastatin or recombinant human granulocyte colony-stimulating factor alone in protecting against stroke-induced damage and could be an optimal therapeutic strategy for stroke.

High oleate is an important seed quality trait frequently incorporated in peanut varieties. Crop wild relatives (CWR) are potentially useful genetic resources for cultivar improvement through genetic introgression; but for wild peanut species, many chemical or nutritional traits are not well characterized. A mutant from Arachis veigae S. H. Santana & Valls (2n = 2x = 20), with increased oleic and very long chain (C ≥ 22) fatty acid content was identified from screening 209 accessions of 45 species using gas chromatography (GC). The A. veigae (formerly A. sylvestris) accession, VVeSv 8373 (PI 688970) contained 55.5% oleic acid in seeds, significantly higher than the average (18.3%) of other accessions within the same species and also significantly higher than the average (37.0%) of all wild peanut accessions evaluated. A C37T substitution was identified by sequencing the coding region of FAD2H, resulting in the nonsense mutation of Q13* (a premature stop codon). This functional mutation may significantly reduce the fatty acid desaturase (FAD) activity and result in the enhanced oleate level. Arachis veigae also contained a high percentage of very long-chain (C ≥ 22) fatty acids, and their variation identified in this study is also discussed and compared with other species. The mutant with such an altered fatty acid composition may be useful for potentially improving seed or food nutrition quality.

Twenty-two health functional legumes and industrial crops contain several phytochemicals and extracts which have potential use as medicinal plants or functional foods in the United States and other countries worldwide. The objective of this study was to present a review of several legume species in the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit’s (PGRCU) collection for potential use as non-traditional human and veterinary medicinal plants. Specific phytochemicals and extracts from various plant organs will be identified and discussed from these legumes and industrial crops. Potential phyto-pharmaceuticals including flavonoids, glycosides, phenolics, cliotides, steroids, and saponin from butterfly pea (Clitoria ternatea L.) flowers, seed coats, and roots; saponin, steroids, anthro-quinones, terpinoids, flavonoids, and phlabotanin from Indigofera cassioides Rottler ex DC. leaves; dequelin, dehydrodeguelin, rotenol, rotenone, tephrosin, and sumatrol from hyacinth bean [Lablab purpureus (L.) Sweet] seeds and roots; L-dopa from velvetbean (Mucuna pruriens (L.) DC. and Sesbania bispinosa (Jacq.) W. Wight seeds; pachyerosin from jicama (Pachyrhizus erosus (L.) Urb. seeds; vitexin from blue wiss [Teramnus labialis (L.f.) Spreng] aerial parts and flavonol glycoside from stems; caffeic, ferulic, cinnamic acids, and kaempferol from mothbean (Vigna aconitifolia (Jacq.) Marechal sprouts; 7S globulins from mungbean (V. radiata (L.) R. Wilczek seeds; defensin, unguilin, trypsin/chymotrypsin inhibitor, 7S globulins from cowpea (V. unguiculata (L.) Walp seeds, and plant extracts. These phytochemicals and extracts have been shown to have multiple potential uses including antifungal, antibacterial, anti-asthmatic, anti-tuberculosis, anti-malaria, Parkinson’s disease management, anti-cancer, antioxidant, oxidative stress reduction, cholesterol reduction, anti-Leishmania amazonensi, anti-breast cancer, anti-inflammatory, skin disease inhibition, reducing blood pressure, immunostimulation, myocardial ischemia protection, anthelmintic, improve eye surface protection from dry eye symptoms, and preventing oral bacteria and kidney damage. These species could provide the human and veterinary medicinal and functional food industries with valuable health products and can be used by other scientist’s and breeders for the development of unique germplasm and/or advanced cultivars with one or more of these traits. Furthermore, many more plant species in the Plant Genetic Resources Conservation Unit (PGRCU) collection need to be evaluated for the identification, quantification, and variability of potentially and very valuable health traits which are currently unknown.

Tomato spotted wilt (TSW) is a serious virus disease of peanut in the United States. Breeding for TSWV resistance would be facilitated by the implementation of marker-assisted selection in breeding programs; however, genes associated with resistance have not been identified. Association mapping is a type of genetic mapping that can exploit relationships between markers and traits in many lineages. The objectives of this study were to examine genetic diversity and population structure in the U.S. peanut mini-core collection using simple sequence repeat (SSR) markers, and to conduct association mapping between SSR markers and TSWV resistance in cultivated peanuts. One hundred and thirty-three SSR markers were used for genotyping 104 accessions. Four subpopulations, generally corresponding to botanical varieties, were classified by population structure analysis. Association mapping analysis indicated that five markers: pPGPseq5D5, GM1135, GM1991, TC23C08, and TC24C06, were consistently associated with TSW resistance by the Q, PCA, Q+K, and PCA+K models. These markers together explained 36.4% of the phenotypic variance. Moreover, pPGPseq5D5 and GM1991 were associated with both visual symptoms of TSWV and ELISA values with a high R2. The potential of these markers for use in a marker-assisted selection program to breed peanut for resistance to TSWV is discussed. Keywords: Association mapping, SSR markers, Tomato spotted wilt virus, Peanuts

A better understanding of the genetic basis that governs the inheritance of biomass quality traits may help to improve sorghum (Sorghum bicolor [L.] Moench) varieties for energy purposes. Here, combining ability studies were conducted using three restorer lines (male) and 60 cytoplasmic male sterile (CMS) lines (female), at two locations in China, during 2017 and 2018. Both entries and environments (i.e., site) significantly affected concentrations of soluble sugar, cellulose, hemicellulose, lignin, and ash of sorghum, in both stems and leaves. The coefficient of variation level was higher in stems than leaves for each chemical component investigated. The broad-sense and narrow-sense heritability indicated the predominance of an additive gene effect upon chemical components occurring in stems and leaves. This investigation is the first report to evaluate the combining ability effects on soluble sugar, cellulose, hemicellulose, lignin, and ash in stems and leaves of sorghum plants. Sorghum exhibited either significantly negative or positive general combining ability (GCA) effect for all chemical components in stems and leaves. Highly significant negative correlations were found between the GCA effect on soluble sugar and that on cellulose, hemicellulose, and lignin. Significant positive correlations were found among GCA effects of cellulose, hemicellulose, and lignin. The GCA effect on ash was significantly negatively correlated with that on soluble sugar but positively so with that on hemicellulose in stems, whereas it had significant negative correlations with that on soluble sugar, cellulose, and hemicellulose in leaves. Based on these findings, 11 and 6 female lines were selected for further development of biomass sorghum hybrids and sweet sorghum hybrids, respectively.

Cowpea (Vigna unguiculata) is an important legume crop with diverse uses. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, a total of 200 genic and 100 genomic simple sequence repeat (SSR) markers were developed from cowpea unigene and genome sequences, respectively. Among them, 27 genic and 27 genomic SSR markers were polymorphic and were used for assessment of genetic diversity and population structure in 105 selected cowpea accessions. A total of 155 alleles and 2.9 alleles per marker were identified, and the average polymorphic information content (PIC) value was 0.3615. The average PIC of genomic SSRs (0.3996) was higher than that of genic SSRs (0.3235), and most of the polymorphic genomic SSRs were composed of di- and trinucleotide repeats (51.9% and 37.0% of all loci, respectively). The low level of detected genetic diversity may be attributed to a severe genetic bottleneck that occurred during the cowpea domestication process. The accessions were classified by structure and cluster analysis into four subgroups that correlated well with their geographic origins or collection sites. The classification results were also consistent with the results from principal coordinate analysis and can be used as a guide during future germplasm collection and selection of accessions as breeding materials for cultivar improvement. The newly developed genic and genomic SSR markers described in this study will be valuable genomic resources for the assessment of genetic diversity, population structure, evaluation of germplasm accessions, construction of genetic maps, identification of genes of interest, and application of marker-assisted selection in cowpea breeding programs.

BackgroundCarica papaya is a trioecious plant species with a genetic sex-determination system defined by sex chromosomes. Under unfavorable environmental conditions male and hermaphrodite exhibit sex-reversal. Previous genomic research revealed few candidate genes for sex differentiation in this species. Nevertheless, more analysis is still needed to identify the mechanism responsible for sex flower organ development in papaya.ResultsThe aim of this study was to identify differentially expressed genes among male, female and hermaphrodite flowers in papaya during early (pre-meiosis) and later (post-meiosis) stages of flower development. RNA-seq was used to evaluate the expression of differentially expressed genes and RT-qPCR was used to verify the results. Putative functions of these genes were analyzed based on their homology with orthologs in other plant species and their expression patterns. We identified a Male Sterility 1 gene (CpMS1) highly up-regulated in male and hermaphrodite flower buds compared to female flower buds, which expresses in small male flower buds (3–8 mm), and that might be playing an important role in male flower organ development due to its homology to MS1 genes previously identified in other plants. This is the first study in which the sex-biased expression of genes related to tapetum development in the anther developmental pathway is being reported in papaya. Besides important transcription factors related to flower organ development and flowering time regulation, we identified differential expression of genes that are known to participate in ABA, ROS and auxin signaling pathways (ABA-8-hydroxylases, AIL5, UPBEAT 1, VAN3-binding protein).ConclusionsCpMS1was expressed in papaya male and hermaphrodite flowers at early stages, suggesting that this gene might participate in male flower organ development processes, nevertheless, this gene cannot be considered a sex-determination gene. Due to its homology with other plant MS1 proteins and its expression pattern, we hypothesize that this gene participates in anther development processes, like tapetum and pollen development, downstream gender specification. Further gene functional characterization studies in papaya are required to confirm this hypothesis. The role of ABA and ROS signaling pathways in papaya flower development needs to be further explored as well.

In this study, the immunoadjuvant effects of recombinant porcine interferon alpha (rPoIFNα) on the killed virus vaccine (KV) of porcine reproductive and respiratory syndrome virus (PRRSV) ...

Two QTLs on ChrB09 significantly associated with both early and late leaf spots were identified by genome-wide association study in the US peanut mini-core collection. Early leaf spot (ELS) and late leaf spot (LLS) are two serious peanut diseases in the USA, causing tens of millions of dollars of annual economic losses. However, the genetic factors underlying resistance to those diseases in peanuts have not been well-studied. We conducted a genome-wide association study for the two peanut diseases using Affymetrix version 2.0 SNP array with 120 genotypes mainly coming from the US peanut mini-core collection. A total of 46 quantitative trait loci (QTLs) were identified with phenotypic variation explained (PVE) from 10.19 to 24.11%, in which eighteen QTLs are for resistance to ELS and 28 QTLs for LLS. Among the 46 QTLs, there were four and two major QTLs with PVE higher than 16.99% for resistance ELS and LLS, respectively. Of the six major QTLs, five were located on the B sub-genome and only one was on the A sub-genome, which suggested that the B sub-genome has more potential resistance genomic regions than the A sub-genome. In addition, two genomic regions on chromosome B09 were found to provide significant resistance to both ELS and LLS. A total of 74 non-redundant genes were identified as resistance genes, among which, twelve candidate genes were in significant genomic regions including two candidate genes for both ELS and LLS, and other ten candidate genes for ELS. The QTLs and candidate genes obtained from this study will be useful to breed peanuts for resistances to the diseases.

Background Sesame (Sesamum indicum) can accumulate over 60% oil in its seed. However, low oil content genotypes with an oil content of less than 50% are also observed. To gain insights into how genes shape this variation, we examined 22 seed and carpel transcriptomes from 3 varieties of sesame with high and low oil content. Results A total of 34.6~52.2% of the sesame genes were expressed with a RPKM greater than 5 in the 22 tissue samples. The expressed gene numbers tended to decrease in the seed but fluctuated in the carpels from 10 to 30 days post-anthesis (DPA). Compared with that of the low oil content sesames, the high oil content sesame exhibited more positive gene expression during seed development. Typically, genes involved in lipid biosynthesis were enriched and could distinguish the high and low genotypes at 30 DPA, suggesting the pivotal role of seed oil biosynthesis in the later stages. Key homologous lipid genes that function in TAG biosynthesis, including those that encoded glycerol-3-phosphate acyltransferase (GPAT), acyl-CoA:diacylglycerol acyltransferase (DGAT), and phospholipid:diacylglycerol acyltransferase (PDAT), were strengthened asynchronously at different stages, but the lipid transfer protein (LTP)-encoding genes, including SIN_1019175, SIN_1019172 and SIN_1010009, usually were highlighted in the high oil content sesames. Furthermore, a list of 23 candidate genes was identified and predicted to be beneficial for higher oil content accumulation. Despite the different gene expression patterns between the seeds and carpels, the two tissues showed a cooperative relationship during seed development, and biological processes, such as transport, catabolic process and small molecule metabolic process, changed synchronously. Conclusions The study elucidated the different expression profiles in high and low oil content sesames and revealed key stages and a list of candidate genes that shaped oil content variation. These findings will accelerate dissection of the genetic mechanism of sesame oil biosynthesis. Electronic supplementary material The online version of this article (10.1186/s12863-019-0747-7) contains supplementary material, which is available to authorized users.

The United States Department of Agriculture–Agricultural Research Service sweetpotato (Ipomoea batatas) germplasm collection contains accessions that were initially collected from various countries worldwide. These materials have been maintained and distributed as in vitro plantlets since the mid-1980s. The status of viral infection by the emerging Sweet potato leaf curl virus (SPLCV) and other Begomovirus spp. in this germplasm has yet to be determined. In order to minimize the potential distribution of virus-infected clones, all accessions in the collection were tested for SPLCV using a real-time polymerase chain reaction assay. In total, 47 of 701 accessions of in vitro plantlets tested positive for SPLCV. The presence of SPLCV detected in these materials was confirmed via biological indexing using the indicator plants I. nil and I. muricata. Symptoms appeared more rapidly on I. muricata than on I. nil. Nucleotide polymorphisms among the isolates were evaluated by sequencing the AV1 coat protein gene from 24 SPLCV-infected accessions. The results revealed that the SPLCV isolates shared high sequence identity. Ten nucleotide substitutions were identified, most of which were synonymous changes. Phylogenetic analysis was conducted on those 24 SPLCV isolates in combination with six described SPLCV species and various SPLCV strains from GenBank to evaluate the relationships among viral species or strains. The results from this analysis indicated that most of the AV1 genes derived from previously classified SPLCV species clustered together, some of which formed well-supported monophyletic clades, further supporting the current taxonomy. Overall, identification of SPLCV-infected germplasm will allow approaches to be employed to eliminate the virus from the collection and limit the distribution of infected materials.

Autophagy exhibits dual effects during viral infections, promoting the clearance of viral components and activating the immune system to produce antiviral cytokines. However, some viruses impair immune defenses by collaborating with autophagy. Mounting evidence suggests that the interaction between autophagy and innate immunity is critical to understanding the contradictory roles of autophagy. Type I interferon (IFN-I) is a crucial antiviral factor, and studies have indicated that autophagy affects IFN-I responses by regulating IFN-I and its receptors expression. Similarly, IFN-I and interferon-stimulated gene (ISG) products can harness autophagy to regulate antiviral immunity. Crosstalk between autophagy and IFN-I responses could be a vital aspect of the molecular mechanisms involving autophagy in innate antiviral immunity. This review briefly summarizes the approaches by which autophagy regulates antiviral IFN-I responses and highlights the recent advances on the mechanisms by which IFN-I and ISG products employ autophagy against viruses.

Sesame (Sesamum indicum L.) is an important oil seed with edible and potentially nutritional and medical uses in most countries and may show variability for bioactive concentrations. The objective of this study was to evaluate seed production weights, numbers, oil, protein, lignan, tocopherol, and fatty acid concentrations in seeds from 8 randomly diverse sesame genotypes with various seed coat colors over two years. Oil analysis were conducted using NMR (nuclear magnetic resonance) on a Bruker mq-one minispec. Protein was measured by combustion on an Elementar Rapid N Exceed nitrogen analyzer. Lignan and tocopherol compounds were prepared and analyzed by HPLC (high performance liquid chromatography) on an Agilent 1100. Fatty acids were separated by gas chromatography on an Agilent 7890A with a 15 m DB23 analytical column and FID (flame ionization detector). The bioactives and 1000 seed weights were significantly influenced by genotype, except for heptadecenoic acid (17:1), while total seed weight, total seed numbers, sesamolin, γ-tocopherol, and oleic acid (18:1) were influenced by year. Oil, protein, δ-tocopherol, and margaric acid (17:0) showed a year x genotype interaction. Significant 1000 seed weights ranged from 1.8 to 3.3 g while oil and protein concentrations significantly ranged from 29.43–54.69% and 13.92–21.76%, respectively. Sesamin and sesamolin ranged significantly from 0.55 to 8.98 mg/g and tocopherols ranged from 0 to 239.58 μg/g. The major unsaturated fatty acids, oleic (18:1) and linoleic (18:2) acids significantly ranged from 26.60 to 54.85 % while the minor unsaturated fatty acids ranged from 0.13 to 0.89 %. The saturated fatty acids significantly ranged from 0 to 10.58 %. Several correlations were observed among the bioactives. The 8 sesame genotypes can be used in breeding programs to develop new cultivars with enhanced bioactives.

Cultivated peanut (Arachis hypogaea L.) is a major oilseed crop providing edible oil and protein. Oil quality is determined by fatty acid composition including the ratio of oleic acid (C18:1) and linoleic acid (C18:2). A genome-wide association study with 13,382 single nucleotide polymorphisms (SNPs) was conducted to investigate the genetics basis of oil, protein, eight fatty acid concentrations, and O/L ratio (ratio of oleic and linoleic acid) using a diverse panel of 120 genotypes mainly selected from the U.S. peanut mini core collection grown in two years. A total of 178 significant quantitative trait loci (QTLs) associated with those seed composition traits were identified with phenotypic variation explained (PVE) from 18.35% to 27.56%. RNA-Seq analysis identified 282 DEGs (differentially expressed genes) within the 1 Mb of the significant QTLs for seed composition traits. Among those 282 genes, sixteen candidate genes for seed fatty acid metabolism and protein synthesis were screened according to the gene functions.

Dry guar (Cyamopsis tetragonoloba L. Taub) seeds are primarily used to extract galactomannan gum for oil fracking, however, the immature pods are used as a vegetable in India and sold in ethnic grocery stores in the Atlanta, Georgia area. Nineteen guar genotypes were grown in the field at Griffin, GA, USA for two years (2010-2011). Since the determination of flavonoid concentration would add value to the guar accessions for use as a functional food vegetable, immature guar pods were evaluated for flavonoid concentration. In this study, the immature pods from these 19 guar accessions were analyzed for flavonoid concentration using high-performance liquid chromatography. Several accessions including PI 253182, PI 262152, PI 263698, and PI 288357 showed significantly greater daidzein concentration than all three controls based on seed production in 2010. However, PI 179926, PI 180434, PI 182969, PI 183400, PI 253182, PI 262152, PI 263882, and PI 263897 exhibited significantly greater genistein concentration than the second and third best controls in 2011. Both PI 180434 and PI 288359 produced significantly higher kaempferol concentration than the third best control. Daidzein concentration was significantly correlated with genistein concentration (r2 = 0.47*) for both years. Luteolin concentration showed a significant negative correlation with genistein (r2 = -0.45*). Quercetin concentration significantly correlated with kaempferol (r2 = 0.854***) and genistein (r2 = 0.455*) concentrations. The accession, PI 542608 was observed to contain high concentrations of kaempferol and quercetin in the cluster analyses. These results will help plant breeders develop guar cultivars with superior flavonoid concentrations.

Protein percentage and mineral concentrations are important parameters for determining the seed nutrition quality. Although the U.S. peanut mini-core collection is the important genetic resources for peanut breeding programs, the variability in protein percentage and mineral concentrations for this mini-core has not been well evaluated. The lack of information may hinder its optimum utilization. The seeds from this mini-core were collected from two field seasons. Their protein percentage and mineral concentrations of 95 accessions were determined by nitrogen analysis and inductively coupled plasma – optical emission spectrometry, respectively. Significant variability in the seed protein percentage among accessions was revealed, ranging from 20.6 to 30.4%, with an average of 26.2%. Significantly higher variability in plant micronutrient mineral concentrations (more than two-fold for B, Cu, Fe, Mn, Mo, Na, Ni, and Zn) than in macronutrient mineral concentrations (less than two-fold for K, Mg, P, and S) was also identified among accessions. Calcium however was an exception, demonstrating 3.7-fold variability among the accessions evaluated. Three accessions (PI 497517, PI 493547, and PI 429429) were identified as lines containing high seed levels of both Fe and Zn. Correlation coefficients were also determined among 28 investigated seed chemical composition traits, using data from a previous study with the same samples. Protein percentage was significantly negatively correlated with seed weight, oil, and oleate percentage. Several mineral elements (Fe, Mg, Mn, and Zn) were also significantly negatively correlated with oleate percentage. The results from this study will be useful for peanut nutrition breeding and food product development.

Sorghum bicolor is cultivated worldwide as a staple food and forage, and is receiving a renewed interest as a bioenergy crop. The objective of this study was to understand the relationships between the function (redox and metal complexation) and structural properties (aromaticity and ionizable functionalities) of (poly) phenolic pigments in the pericarp of sorghum grain which will ultimately control its antioxidant and bird/mold resistance behaviors. As compared to white seeds lacking condensed tannins, brown seeds (with and without pigmented testa) contained (i) 0.08-0.01 wt% cyanidin-equivalent condensed tannins, (ii) higher aromaticity (which decreases the reduction potential of polyphenols), and (iii) as much as 6-fold greater FeIII reduction capacity. The degree of aromaticity was determined by (i) UV absorbance at 360 nm and (ii) fluorescence excitation-emission (EEM) peak position. Basic (0.1 M NaOH) extracts of all seeds contained EEM peaks (230/330 and 280/330) attributable to protein. Addition of FeIII resulted in a new aromatic EEM peak (320/440) only for the brown seeds which could be used as a fingerprint for the redox and coordination chemistry of sorghum grain pigments. Key words: Proanthocyanidin, cereal, sweet sorghum, colorimetric method, transition metal.

Niger (Guizotia abyssinica, L.) is a desirable oilseed crop for birdseed, especially for finches (Spinusspp.) because of its high ratio of unsaturated to saturated fatty acids and relatively high oil content. In 2012, phenotypic traits, seed oil and fatty acid content measurements were made on 14 plant introductions (PIs) from the United States Department of Agriculture germplasm collection. The PIs originated in Ethiopia (ten), India (three) and USA (one). The phenotypic traits analysed included seed/plant, branches/plant, capitula/plant1, average seed/capitulum and plant height. After initial assessments of the 14 PIs, three were selected for use as parents to produce two one-way and two two-wayF1crosses for the purpose of evaluating self-incompatibility (SI). Parent andF1progeny seeds were planted in a greenhouse and transplanted to a field site at the East Tennessee Research and Education Center (2012, 2013 and 2014). Comparisons from 2012 showed seed oil of the 14 PIs ranging from 32.9 to 37.9% (PI 508076 (Ethiopia) and PI 509436 (India), respectively). Major fatty acids included stearic, palmitic, oleic and linoleic; with linoleic acid in highest amount. PI508079 (Ethiopia) had the best combination of seed yield, seed oil and linoleic acid content. Over 2013 and 2014, SI ranged from 91.1 to 100.0%. W6 18860 (USA) had the most self-compatibility, and theF1plants generated from crosses between W6 18860 and other plants tended to be self-compatible when the former was used as a pollen recipient. The results obtained from this study should be useful for niger breeding and production purposes.

Our previous research obtained purified recombinant porcine interferon-α (rPoIFN-α) containing thioredoxin (Trx) fusion tag in E. coli Rosetta (DE3). Here, we evaluate the efficacy of this rPoIFN-α to prevent piglets from the infection of the transmissible gastroenteritis virus (TGEV) attack. In this experiment, twenty-five TGEV-seronegative piglets were randomly divided into five groups. Group 1 was positive control and only challenged with TGEV; Pigs in groups 2-4 were pretreated with 2 × 10(7)IU/pig, 2 × 10(6)IU/pig, and 2 × 10(5)IU/pig rPoIFN-α before TGEV challenge. The fifth group is a negative control group. The animals of this group are pretreated only with Trx protein-containing PBS solution without TGEV challenge. After 48 h of rPoIFN-α pretreatment, the pigs in groups 1-4 were challenged by TGEV, and the pigs in group 5 were administered with PBS. The surveillance results show that Pigs pre-treated with 2 × 10 (7) IU/pig rPoIFN-α are fully aligned with the violent TGEV attack. Pigs pretreated with 2 × 10 (6) IU/pig rPoIFN-α are partially aligned with the violent TGEV attack. Though piglets pretreated with 2 × 10(6) IU/pig or 2 × 10(5)IU/pig rPoIFN-α cannot be adapted to the challenge of TGEV. However, the use of this dose of rPoIFN-α could put off the clinical signs of pigs than the positive control group of the above. These results indicate that rPoIFN-α can protect pigs from the infection of potential TGEV or delay the appearance of clinical symptoms, and its effect is dose-dependent.

Bamboo shoots and leaves are valuable food sources for both humans and livestock. The USDA-ARS NPGS (National Plant Germplasm System) collections hold 93 bamboo species in 20 genera. Total leaf protein, amino acid composition and elemental content for these important genetic resources had never been quantified. Lack of nutrition information hinders germplasm utilization. The above-mentioned nutritional traits were evaluated from these 93 species in this study. Leaf protein content among bamboo species ranged from 8.12 to 16.33% with an average of 12.84%. This average was higher than 9.0% observed for switchgrass leaves, but considerably lower than 32.48% in cassava leaves. For 18 quantified amino acids, there was more than a twofold variation among the samples evaluated. For 12 quantified mineral elements, there was significant variability from the low end (4.2-fold, 2.27–9.52 mg/g calcium; 4.4-fold, 56.17–246.43 µg/g sodium) to the high end (61.5-fold, 17.67–1087.0 µg/g manganese; 40.8-fold, 42.0–1713.5 µg/g aluminium). Due to their variability in leaf nutritive value, bamboo species should be carefully chosen when they are used as a feedstock. The results from this study will be useful for the bamboo industry, producers and consumers.

Sorghum [Sorghum bicolor (L.) Moench] is a high-yielding C4 crop used not only to produce grains for food, feed, and industrial uses but also biomass (i.e., leaf and stem) for biofuel production. To take better advantage of its heterosis for both grain and biomass dual-purpose use, the combining ability of 34 cytoplasmic male sterile lines (female) were tested with 3 cytoplasmic male fertile restore lines (male) using the North Carolina design (NCⅡ) at Zhuozhou (Hebei province) and Jiexiu (Shanxi province) in northern China for two years (2017 and 2018). The hybrids exhibited a grain yield of 0.3 ∼ 14.0 t ha−1 and had an aboveground biomass yield (AGBY) of 9.6 ∼ 109.9 t ha−1 across both sites in 2017 and 2018. The genotype and site × genotype interactions significantly affected the yield and agronomic traits. With respect to their grain and biomass dual-purpose use, the tested 34 female lines revealed that plant height, gravity center height, productive tiller rate, and harvest index were strongly general combining ability (GCA) sensitive. Stem width, days to maturity, AGBY, and grain width were medium GCA-sensitive; and grain yield, 100-grain weight, days between heading and maturity, and grain bulk density were weakly GCA-sensitive. The GCA effect on grain yield was positive and significantly correlated with productive tiller rate, AGBY, and harvest index. The GCA effect on AGBY had a positive, significant correlation with plant height, gravity center height, productive tiller rate, and days to maturity; but the effect was negatively correlated with 100-grain weight and grain width. For tested traits, the additive gene effects strongly predominated over the non-additive genes for tested traits. Plant height was the most GCA-sensitive trait and the most important for biomass production. Female lines AMP418, AMP431, AMP434, AMP443, AMP495, AMP496 and the male line X097 were selected as being high-GCA effect germplasm. These selections from newly introduced cytoplasmic male sterile lines hold promise for accelerating the genetic improvement of sorghum for its dual-purpose use as grain for food and biomass for biofuel.

Soybean [Glycine max (L.) Merr.] was domesticated from wild soybean (G. soja Sieb. and Zucc.) and has been further improved as a dual-use seed crop to provide highly valuable oil and protein for food, feed, and industrial applications. However, the underlying genetic and molecular basis remains less understood. Having combined high-confidence bi-parental linkage mapping with high-resolution association analysis based on 631 whole sequenced genomes, we mapped major soybean protein and oil QTLs on chromosome15 to a sugar transporter gene (GmSWEET39). A two-nucleotide CC deletion truncating C-terminus of GmSWEET39 was strongly associated with high seed oil and low seed protein, suggesting its pleiotropic effect on protein and oil content. GmSWEET39 was predominantly expressed in parenchyma and integument of the seed coat, and likely regulates oil and protein accumulation by affecting sugar delivery from maternal seed coat to the filial embryo. We demonstrated that GmSWEET39 has a dual function for both oil and protein improvement and undergoes two different paths of artificial selection. A CC deletion (CC-) haplotype H1 has been intensively selected during domestication and extensively used in soybean improvement worldwide. H1 is fixed in North American soybean cultivars. The protein-favored (CC+) haplotype H3 still undergoes ongoing selection, reflecting its sustainable role for soybean protein improvement. The comprehensive knowledge on the molecular basis underlying the major QTL and GmSWEET39 haplotypes associated with soybean improvement would be valuable to design new strategies for soybean seed quality improvement using molecular breeding and biotechnological approaches., Author summary We map highly effective protein and oil QTLs to a seed coat-preferentially expressed sugar transporter (GmSWEET39) gene by a combination of association analysis based on 631 whole-genome sequencing data and a bi-parental linkage mapping, proving that GmSWEET39 has pleiotropic associations with two of the most important soybean traits, seed protein and oil. A 2-bp (CC) deletion in GmSWEET39 is associated with higher seed oil and lower seed protein, and has been extensively selected and used worldwide, likely for higher oil. The intensive use or fixation of the CC deletion in soybean breeding result in low protein in current soybean cultivars, which is a big problem facing the current soybean industry. The knowledge about the genetic basis and identification of two major haplotypes for high protein and high oil should be highly significant to address the issue related to low protein in the current soybean industry and meet dramatically increasing need for plant-based protein in the food industry. Our successful integrative and "big-data-driven” approach, which uses the huge amount of genome and transcriptome sequencing and phenotypic data available in the community, should provide an effective case study for post-genomic data-driven research.

Control of currently circulating re-assorted low-pathogenicity avian influenza (LPAI) H9N2 is a major concern for both animal and human health. Thus, an improved LPAI H9N2 vaccination strategy is needed to induce complete immunity in chickens against LPAI H9N2 virus strains. Cytokines play a crucial role in mounting both the type and extent of an immune response generated following infection with a pathogen or after vaccination. To improve the efficacy of inactivated LPAI H9N2 vaccine, prokaryotic expression recombination chicken interferon-α (rchIFN-α) was used as vaccine adjuvant.In this study chIFN-α was used as adjuvant in inactivated AI H9N2 vaccine, modulated the immune response of chickens against the vaccine antigen through enhanced humoral and Th1-biased cell-mediated immunity, compared to chickens that received single AI H9N2 vaccine. To further test the protective efficacy of this improved vaccination regimen, immunized chickens were challenged with a high dose of LPAI H9N2 virus. Combined administration rchIFN-α showed markedly enhanced protection compared to single administration of the vaccine, as determined by mortality, clinical severity, and feed and water intake. This enhancement of protective immunity was further confirmed by reduced rectal shedding and replication of AIV H9N2 in challenged chickens. Our results indicate the value of combined administration of rchIFN-α to generate an effective immunization strategy in chickens against LPAI H9N2.

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome ofAnanas comosusvar.bracteatusCB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89Ananasgenomes. Cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixture, while ‘Singapore Spanish’ supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.

The original version of this article unfortunately contained an error in the number of unigenes reported in the Result section of Molecular Breeding article, “Development of SSR markers and assessment of genetic diversity of adzuki bean in the Chinese germplasm collection” (Mol Breeding (2015) 35:191, DOI https://doi.org/10.1007/s11032-015-0383-5 ).

The level of oleic acid in peanut seed is one of the most important factors in determining seed quality and is controlled by two pairs of homeologous genes (FAD2A and FAD2B). The genotypes of eight F8 breeding lines were determined as AABB, aaBB, AAbb, and aabb by real-time polymerase chain reaction and sequencing. Fresh seeds were collected from five seed developmental stages and, after drying, were used for chemical analysis. Our results showed that (1) as seeds developed, seed weight, oil content, and oleic acid level significantly increased, whereas four other fatty acid levels decreased, but protein content and another four fatty acid levels did not significantly change, (2) FAD2A/FAD2B significantly affected fatty acid profiles but not oil and protein contents, and (3) the data were consistent across 2 years. The variability of seed quality traits revealed here will be useful for peanut breeders, farmers, processers, and consumers.

In order to produce clean energy from renewable lignocellulosic biomass, the feedstock must be pretreated by means of one or combined cost-competitive methods to make the entire process economically feasible. Fungal cultivation may be one promising pretreatment approach, for which the effectiveness varies with different fungal strains in regard to biomass loss, sugar yield, enzyme loading, and co-product yield. Wild-type fungus might have a great potential in pretreating feedstock for both lowered enzyme loading and beneficial co-product enzyme production. In this study, 25 diverse fungal strains were screened for pretreatment of switchgrass biomass with regard to co-production of beneficial enzymes and the subsequent saccharification process, by examining switchgrass biomass loss, effectiveness of enzymatic hydrolysis, and ligninolytic activity. The most promising fungus was identified as an inedible mushroom, Agaricus molybdites (H4) with the highest saccharification efficiency and ligninolytic enzyme production. Additionally, eight accessory enzymes, e.g. pectinase, esterase, xylanase, β-glucosidase, chitinase, lipase, α-amylase, and laccase, were found to assist cellulase in enhancing saccharification of H4 pretreated switchgrass to varying degrees. Our experimental results suggest that pretreatment of switchgrass with an appropriate fungus, followed by exposure to cellulase and synergistic accessory enzymes can be an effective strategy for maximizing the process of saccharification.

Higher plants use RNA silencing to defend against viral infections. As a counter defense, plant viruses have evolved proteins that suppress RNA silencing. Mealybug wilt of pineapple (MWP), an important disease of pineapple, has been associated with at least three distinct viruses, Pineapple mealybug wilt associated virus -1, -2, and -3 (PMWaV-1, -2, and -3). Selected open reading frames (ORFs) of PMWaV-1 and PMWaV-2 were screened for their local and systemic suppressor activities in Agrobacterium-mediated transient assays using green fluorescent protein (GFP) in Nicotiana benthamiana. Results indicate that PMWaV-2 utilizes a multiple-component RNA silencing suppression mechanism. Two proteins, p20 and CP, target both local and systemic silencing in N. benthamiana, while the p22 and CPd proteins target only systemic silencing. In the related virus PMWaV-1, we found that only one of the encoded proteins, p61, had only systemic suppressor activity. Of all the proteins tested from both viruses, only the PMWaV-2 p20 protein suppressed local silencing induced by double-stranded RNA (dsRNA), but only when low levels of inducing dsRNA were used. None of the proteins analyzed could interfere with the short distance spread of silencing. We examined the mechanism of systemic suppression activity by investigating the effect of PMWaV-2-encoded p20 and CP proteins on secondary siRNAs. Our results suggest that the PMWaV-2 p20 and CP proteins block the systemic silencing signal by repressing production of secondary siRNAs. We also demonstrate that the PMWaV-2 p20 and p22 proteins enhanced the pathogenicity of Potato virus X in N. benthamiana.

Transgenic pineapple plants have been produced for the purpose of improving various economically important traits. The efforts have focused on traits such as natural flowering control, herbicide tolerance for weed control, disease and nematode control, and fruit quality traits. The fruit quality traits include increased iron and zinc levels, chilling-induced fruit browning, and increased carotenoids. Numerous constructs and approaches have been used in this normally vegetatively propagated crop. The major bottleneck for high-throughput gene functional analyses of pineapple is nucleic acid delivery and tissue culture/regeneration system. Though tissue culture is widely used commercially to increase planting material, this is slow, and the development of a plantlet following transformation culture has shown significant varietal differences and somaclonal variation. In this chapter, we focus on reviewing the technical aspects of the published transformation processes with the intention to provide practical information for planning pineapple transformation experiments.

Bamboo shoots and leaves are nutritious, providing food for human and animal consumption. However their nutrient value depends on a number of factors including the bamboo species (e.g. taxon), harvesting season and growing location. Leaf crude protein content, amino acid composition and mineral element concentration were quantified from leaf samples collected from 222 accessions representing two bamboo types (temperate/tropical), two growing seasons (dry/wet) and three locations (PGRCU-Byron, GA; TARSMayaguez, PR; and Govardhan Gardens-Mayaguez, PR). Significant variability in leaf nutrient value was identified among accessions, types, growing locations and harvesting seasons. On average, bamboo leaf tissue contained 12.92% protein with relatively high percentages of leucine (Leu, 8.97%) and proline (Pro, 7.98%) and low percentages of tryptophan (Trp, 1.69%) and histidine (His, 2.01%). Bamboo leaves also contained relatively high concentrations of the macro-mineral elements potassium (K, 12.17mg/g) and calcium (Ca, 5.37mg/g), high concentrations of the micro-mineral elements manganese (Mn, 388.76 μg/g) and iron (Fe, 123.19 μg/g), and low concentrations of boron (B, 7.8 μg/g) and zinc (Zn, 28.56 μg/g). PI 647932 and TARS 182857 contained the highest and lowest protein content (21.69% and 5.78%), respectively. Temperate bamboos contained a significantly higher percentage of protein (13.02%) than tropical bamboos (12.71%). Leaf samples harvested from the dry season contained a significantly higher percentage of protein (13.12%) than leaf samples harvested from the wet season (12.70%). The leaf samples harvested from Govardhan Garden location contained a higher percentage of protein (13.40%) than from Byron (12.65%) and TARS (12.89%) locations. The leaf samples harvested from Govardhan Garden contained a significantly higher iron concentration (151.22 μg/g) than from the other two locations (118.19 μg/g, 111.52 μg/g), whereas the leaf samples collected from Byron contained a significantly higher zinc concentration (36.03 μg/g) than what was observed from the other two locations (27.83 μg/g, 22.11 μg/g). There was no significant difference in iron and zinc concentrations between leaf samples collected from dry or wet seasons. Tropical bamboo leaves contained a higher iron concentration (131.74 μg/g) than temperate bamboo leaves (118.95 μg/g), whereas temperate bamboo leaves contained a significantly higher zinc concentration (29.82 μg/g) than tropical bamboo leaves (26.01 μg/g). The information on the bamboo leaf nutrient value related to bamboo accessions, types, growing location and harvesting season will be very useful for bamboo growers, processors and consumers.

Sesame germplasm harbors genetic diversity which can be useful for sesame improvement in breeding programs. Seven accessions with different levels of oleic acid were selected from the entire USDA sesame germplasm collection (1232 accessions) and planted for morphological observation and re-examination of fatty acid composition. The coding region of the FAD2 gene for fatty acid desaturase (FAD) in these accessions was also sequenced. Cultivated sesame accessions flowered and matured earlier than the wild species. The cultivated sesame seeds contained a significantly higher percentage of oleic acid (40.4%) than the seeds of the wild species (26.1%). Nucleotide polymorphisms were identified in the FAD2 gene coding region between wild and cultivated species. Some nucleotide polymorphisms led to amino acid changes, one of which was located in the enzyme active site and may contribute to the altered fatty acid composition. Based on the morphology observation, chemical analysis, and sequence analysis, it was determined that two accessions were misnamed and need to be reclassified. The results obtained from this study are useful for sesame improvement in molecular breeding programs.

Teramnus labialis and T. uncinatus are both underutilized legume species. Teramnus labialis is used as food in India while T. uncinatus has potential use in pasture mixes. Photoperiod-sensitive Teramnus accessions were grown in the greenhouse from 2010 to 2011 and evaluated for flavonol content, oil%, and fatty acid compositions. Significant variations for seed numbers produced, flavonol content, oil%, and fatty acid compositions were detected. Seed numbers ranged from 16 to 3,792 in both species. Teramnus accessions produced more quercetin (ranging from 0.615 to 2.228 mg/g) in their seeds than the other flavonols. However kaempferol and isorhamnetin content ranged from 0 to 0.066 and 0 to 0.086 mg/g (dry seed weight basis), respectively among all accessions. Oil% ranged from 2.65 to 5.64% and more oleic, linoleic, and linolenic acids ranging from 6.69 to 25.97, 31.82 to 41.44, and 17.7 to 32.66%, respectively, were produced among all Teramnus accessions. The seeds from all Teramnus accessions also produced the least saturated fatty acid compositions (ranging from 0.08 to 15.36%). Several significant correlations were also detected for these traits among the accessions. Quercetin showed highly significant positive correlations with kaempferol (r = 0.59, p.0001), oil% (r = 0.58, p.0001), and oleic acid (r = 0.31, p.001). Quercetin also showed a significant negative correlation with linoleic acid (r = -0.49, p.0001). These correlations are important because useful breeding procedures could be conducted on improving flavonol, oil%, and fatty acid compositions in Teramnus labialis and T. uncinatus accessions.

Some Senna species are important medicinal plants used worldwide and may show variation for sennoside concentrations. The USDA, ARS, PGRCU (United States Department of Agriculture, Agricultural Research Service, Plant Genetic Resources Conservation Unit) curates several Senna species including candlebush [S. alata (L.) Roxb.], Alexandrian senna [S. alexandrina Mill.], S. angulata (Vogel) H.S. Irwin & Barneby, S. covesii (A. Gray) H.S. Irwin & Barneby, S. hirsuta var. hirta H.S. Irwin & Barneby, S. hirsuta var. leptocarpa (Benth.) H.S. Irwin & Barneby, S. occidentalis (L.) Link, and S. uniflora (Mill.) H.S. Irwin & Barneby. The natural products including sennoside A and B are the primary laxative ingredients in many medicinal products. However, it is unknown if sennoside A and B are found in many of these Senna species and at what concentrations. The objective of this study was to evaluate sennoside A and B content from leaves of 14 and pods of four accessions including eight Senna species over two years and locations. Sample analysis was performed by HPLC (high performance liquid chromatography) on an Agilent 1100 with an auto-sampler and diode array detector. Significant accession and location x accession effects were observed for sennoside A and B. Mean separations revealed that leaves from S. alata produced significantly more sennoside A (8.55 mg/g) than all other species. However, immature pods from S. alexandrina produced the significantly highest sennoside B (16.19 mg/g) content. While this is a preliminary analysis, it provides evidence for higher levels of sennoside A and B in S. alata and S. alexandrina than in S. angulata, S. covesii, S. hirsuta var. hirta, S. hirsuta var. leptocarpa, S. occidentalis, and S. uniflora. These results show that both S. alata and S. alexandrina produced the highest sennoside concentrations. However, additional studies are required to verify sennoside content in other Senna species and organs including Senna pods.

A late fall frost may significantly affect sugar crops’ stem sugar composition, yield and juice quality for biofuel and bioproduct manufacture. Research on the effects of late fall frost in sugarcane is well documented, but information is lacking for sweet sorghum. Three and six commercial cultivars of sugarcane and sweet sorghum, respectively, were selected and evaluated for exposure to a late fall frost (-2.8&degC) in Griffin, Georgia, USA. Under the same controlled environmental conditions in a screen house, the late fall frost induced more damage to sugarcane than sweet sorghum stems. The frost caused damage to sugarcane tissue and for juice to exude from stems, whereas similar behavior was not observed for sweet sorghum. In both sugarcane and sweet sorghum, the glucose/fructose ratio was significantly reduced, but this change may not be totally directly related to the frost effect. Overall, these initial results suggest that sweet sorghum may have a better tolerance to fall frost than sugarcane. Two sweet sorghum cultivars, Grassl and M81E, responded well to the late fall frost, and they can possibly be used as feedstocks for biofuel/bioproduct manufacture in areas susceptible to frosts including northern regions of the Southeastern US.

Several Desmodium species are adapted to the environment of Griffin, Georgia, USA. The determination of flavonoid concentrations, oil content and fatty acid compositions of 25 Desmodium accessions representing five species (D. discolor Vogel, D. incanum (G.Mey.) DC., D. intortum (Mill.) Urb., D. sandwicense E. Mey. and D. tortuosum (Sw.) DC.) would add value to the members of the genus Desmodium for possible use as livestock health supplements. In this study, the seeds of these 25 accessions were evaluated for flavonoid concentrations, oil content and fatty acid compositions using high-performance liquid chromatography, nuclear magnetic resonance and gas chromatography, respectively. Several accessions exhibited significantly greater values for all the traits than the controls. The Desmodium accessions produced significantly greater concentrations of quercetin and kaempferol than the best control accession (D. incanum, PI 477072). However, all the Desmodium accessions produced significantly greater concentrations of isorhamnetin and luteolin than the control accessions. All the Desmodium accessions had greater linoleic (18:2) and behenic (22:0) acid content than a couple of D. incanum control accessions in 2010 and 2011. Significant correlations were observed between several traits. The concentration of quercetin was significantly correlated with that of kaempferol (r2= 0.69***); however, the concentration of quercetin exhibited a significantly negative correlation (r2= − 0.41*) with that of isorhamnetin. Oil content was significantly correlated with palmitic acid (r2= 0.61**), stearic acid (r2= 0.81***), linolenic acid (r2= 0.58**) and lignoceric acid (r2= 0.80***) content. This information will assist breeders and other scientists in developing superior cultivars with optimum levels of flavonoid concentrations, oil content and fatty acid compositions for many of these Desmodium species.

Horse gram [Macrotyloma uniflorum (Lam.) Verdc.] seeds containing high concentrations of fatty acids, flavonols and minerals should provide government, public and private organizations with a nutritious and healthy food for use by malnourished and food deprived people worldwide. Seeds from seven horse gram accessions, geographically adapted to Griffin, GA, USA were analyzed for fatty acid, flavonol, and mineral concentrations using gas chromatography, reverse-phase high performance liquid chromatography, and inductively coupled plasma-optical emission spectroscopy, respectively. Significant year effects occurred for stearic, oleic, linoleic, arachidic, gadoleic, and lignoceric acids. Oleic, linoleic, and linolenic acid ranged from 8.9%–16.8%, 40.3%–45.6%, and 11.6%–14.3%, respectively, as percent of total fatty acids measured (total oil ranged from 2.32% to 2.87%). Seed concentrations of myricetin, quercetin, and kaempferol ranged from 0–36 μg/g DW, 0–27 μg/g DW, and 240–316 μg/g DW, respectively and the only year effect was observed for kaempferol among the horse gram accessions. Year effects were found for Fe, K, Mg, Mn, Ni, and S. Mean concentrations of macrominerals (Ca, K, Mg, P, and S) and microminerals (Cu, Fe, Mn, Ni, and Zn) ranged from 1.3–14 mg/g DW, and 1.0–95.0 μg/g DW, respectively. Several correlations were observed among several fatty acids, flavonols, and minerals. The mono-unsaturated fatty acid, oleic acid correlated significantly with linoleic acid (r = −0.64), arachidic acid (r = −0.61), Ca (r = 0.50) and Zn (r = 0.51, all at P < 0.01). The flavonol, myricetin correlated significantly with quercetin (r = 0.92, P < 0.0001), while quercetin correlated with Ca (r = 0.82, P < 0.0001) and kaempferol correlated with Mg (r = 0.61, P < 0.01). Several mineral correlations were found including Fe with K (r = 0.66) and Mg (r = 0.56, both at P < 0.01). These seven horse gram accessions can be used in breeding programs to facilitate the production of superior cultivars with favorable fatty acid profiles, flavonol content, and mineral compositions.

Objective: Seedling cold tolerance is one of the important traits for sweet sorghum production. This study is to evaluate the method for identification of sweet sorghum accessions with seedling cold tolerance using both lab cold germination and field early-spring cold planting. Methodology: Sorghum seeds were germinated in growth chamber (under lab cold condition) at a constant 12°C for five weeks. After two weeks, germinated seeds and germination rates were counted and calculated at weekly intervals for four times. The same seed lots for lab cold test were also planted 45 days earlier than the normal planting time in the field (early-spring cold planting). In addition to seedling dry weight, germinated seeds and seed germination rates were also counted and calculated at weekly intervals for three times. Results: In this study, a high correlation coefficient between lab germination rate and field germination rate (R2=0.503, p

The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were used to study nucleotide diversity and population structure in the X-linked region. Diversity is very low for all genes in the X-linked region in the wild dioecious population, with nucleotide diversity π syn = 0.00017, tenfold lower than the autosomal region (π syn = 0.0017) and 12-fold lower than the Y-linked region (π syn = 0.0021). Analysis of the X-linked sequences shows an undivided population, suggesting a geographically wide diversity-reducing event, whereas two subpopulations were observed in the autosomes separating gynodioecy and dioecy and three subpopulations in the Y-linked region separating three male populations. The extremely low diversity in the papaya X-linked region was probably caused by a recent, strong selective sweep before domestication, involving either the spread of a recessive mutation in an X-linked gene that is beneficial to males or a partially dominant mutation that benefitted females or both sexes. Nucleotide diversity in the domesticated X samples is about half that in the wild Xs, probably due to the bottleneck when hermaphrodites were selected during domestication. The extreme low nucleotide diversity in the papaya X-linked region is much greater than observed in humans, great apes, and the neo-X chromosome of Drosophila miranda, which show the expected pattern of Y-linked genes

The 7.4 million plant accessions in gene banks are largely underutilized due to various resource constraints, but current genomic and analytic technologies are enabling us to mine this natural heritage. Here we report a proof-of-concept study to integrate genomic prediction into a broad germplasm evaluation process. First, a set of 962 biomass sorghum accessions were chosen as a reference set by germplasm curators. With high throughput genotyping-by-sequencing (GBS), we genetically characterized this reference set with 340,496 single nucleotide polymorphisms (SNPs). A set of 299 accessions was selected as the training set to represent the overall diversity of the reference set, and we phenotypically characterized the training set for biomass yield and other related traits. Cross-validation with multiple analytical methods using the data of this training set indicated high prediction accuracy for biomass yield. Empirical experiments with a 200-accession validation set chosen from the reference set confirmed high prediction accuracy. The potential to apply the prediction model to broader genetic contexts was also examined with an independent population. Detailed analyses on prediction reliability provided new insights into strategy optimization. The success of this project illustrates that a global, cost-effective strategy may be designed to assess the vast amount of valuable germplasm archived in 1,750 gene banks.

BACKGROUND: In spite of increasing knowledge of allelopathic rice as an efficient component involved in paddy weed management, relatively little is known about its reproduction in response to competing weeds. Reproduction allocation of individual allelopathic rice plants in relation to monoculture and mixed culture with competing barnyardgrass in a paddy field was studied, along with analyses of soil nutrients and microbial communities to understand the potential mechanism. RESULTS: At a 1:1 barnyardgrass and rice mixture proportion identified from a replacement series study, biomass, grain yield and major parameters of individual allelopathic rice plants at the mature stage were increased by competing barnyardgrass. There was no difference in allelopathic rice root-zone soil ammonium N and Olsen P between monoculture and mixed culture. However, mixed culture altered soil microbial biomass C and communities. When mixed with barnyardgrass, allelopathic rice root zone had an 87% increase in soil microbial biomass C. Phospholipid fatty acid (PLFA) profiling indicated that the signature lipid biomarkers of bacteria, actinobacteria and fungi were affected by mixed culture. Principal component analysis clearly identified differences in the composition of PLFA in different soil samples. CONCLUSION: Allelopathic rice specific changes in soil microbial communities may generate a positive feedback on its own growth and reproduction in the presence of competing barnyardgrass in a given paddy system. Copyright © 2012 Society of Chemical Industry

A key step during crop domestication is the loss of seed shattering. Here we show that seed shattering in sorghum is controlled by a single gene, Shattering1 (Sh1), which encodes a YABBY transcription factor. Domesticated sorghums harbor three different mutations at the Sh1 locus. Variants at regulatory sites in the promoter and intronic regions lead to a low level of expression, a 2.2-kb fragment deletion causes a truncated transcript that lacks the second and third exons, and a GT-to-GG splicing variant in the intron 4 results in removal of the exon 4. The distributions of these non-shattering haplotypes among sorghum landraces suggest three independent origins. The function of the rice ortholog (OsSh1) was subsequently validated with a shattering resistant mutant, and two maize orthologs (ZmSh1-1 and ZmSh1-5.1+ZmSh1-5.2) were verified with a large mapping population. Our results indicate that Sh1 genes for seed shattering were under parallel selection during sorghum, rice, and maize domestication.

Papaya is a major fruit crop in tropical and subtropical regions worldwide. It has long been recognized as a nutritious and healthy fruit rich in vitamins A and C. Its small genome, unique aspects of nascent sex chromosomes, and agricultural importance are justifications for sequencing the genome. A female plant of the transgenic variety SunUp was selected for sequencing its genome to avoid the complication of assembling the XY chromosomes in a male or hermaphrodite plant. The draft genome revealed fewer genes than sequenced genomes of flowering plants, partly due to its lack of genome wide duplication since the ancient triplication event shared by eudicots. Most gene families have fewer members in papaya, including significantly fewer disease resistance genes. However, striking amplifications in gene number were found in some functional groups, including MADS-box genes, starch synthases, and volatiles that might affect the speciation and adaptation of papaya. The draft genome was used to clone a gene controlling fruit flesh color and to accelerate the construction of physical maps of sex chromosomes in papaya. Finishing the papaya genome and re-sequencing selected genomes in the family will further facilitate papaya improvement and the study of genome and sex chromosome evolution in angiosperms, particularly in Caricaceae.