Development of structured populations and breeding lines for trait analysis and improved varieties in Bambara Groundnut (Vigna subterranea L. Verdc)

Underutilised crop species have the potential to contribute significantly to increased crop diversity and to improved food and nutrition security worldwide. Bambara groundnut [Vigna subterranea (L.) Verdc.] is an underutilised, protein-rich and self-pollinating legume, which can withstand high temperatures and drought stress, and mainly grown in semi-arid Africa. The crop is still largely grown as landraces (a mixture of genotypes) and has limited established structured populations and breeding lines due to a lack of genetic improvement activities and commercial interests. Twelve genotypes of bambara groundnut collected from East, West and Southern Africa and Southeast Asia were used to evaluate the variation in phenotypic traits and the correlation between the observed variation and the landraces’ geographical origins in randomised complete block design (RCBD). All phenotypic traits in the twelve genotypes were significantly influenced (p < 0.01) by genotypes. Principal component analysis (PCA) showed that PC1 accounted for 97.33% of the variation and was associated with four genotypes collected from East and Southern Africa. PC2 accounted for 2.48% of the variation and was associated with five genotypes collected from East, West and Southern Africa. The variation observed within the twelve genotypes of bambara groundnut provides a breeding resource pool for use in controlled crossing to develop ideotypes with desirable phenotypic traits, i.e., high harvest index, 100-seed weight, early days to flowering or short life cycle. Two F2 bi-parental segregating populations of bambara groundnut derived from different geographical origins, IITA-686 (Tanzania, East Africa) × Tiga Nicuru (Mali, West Africa) and S19-3 (Namibia, Southern Africa) × DodR (Tanzania, East Africa) were developed to obtain structured populations and breeding lines for genetic analysis and trait dissection. Transgressive segregation for a number of traits was observed in the two F2 bi-parental populations, as some individual lines in the segregating populations showed trait values greater or less than their parents. The variability between the two F2 bi-parental segregating populations and the negative relationship between morphological traits and yield-related traits provide resources for development of structured populations and selection of breeding lines for bambara groundnut breeding programme. Assessment of segregating populations for their ability to withstand drought stress conditions is one of the best approaches to develop breeding lines and drought-tolerant varieties. The genotype S19-3 exhibits short life cycle and is considered as drought resistant landrace while DodR is reported to have comparatively high 100-seed weight and yield. A total of 114 individual lines derived from S19-3 × DodR were advanced into F3 and F4 segregating populations and examined in a rainout shelter to identify superior lines under drought stress. Drought stress significantly reduced (p < 0.05) shoot dry weight, seed weight per plant, harvest index, shelling percentage, chlorophyll content index and quantum yield PSII photochemistry (FV/FM) in the F3 and F4 segregating populations of bambara groundnut. Stomatal conductance, photosynthesis rate, transpiration rate and intracellular CO2 were significantly reduced (p < 0.05) while leaf water use efficiency was significantly increased (p < 0.05) towards the end of the drought stress period in the F4 segregating population. Individual lines with higher chlorophyll content index, quantum yield PSII photochemistry (FV/FM), relative water content, stomatal conductance, leaf water use efficiency, seeds weight per plant and harvest index were identified. These individuals could be selected as superior lines for genetic analysis and variety development for drought adaption. In order to dissect the complexity of drought resistance, the inheritance of yield-related and morphological traits and to use genomic tools for yield enhancement of bambara groundnut under drought-stressed conditions, a genetic linkage map covering 1,040.92 cM across 11 linkage groups was constructed using 228 DArTseq markers in the F2 segregating population derived from S19-3 × DodR. Significant QTLs for shoot dry weight were mapped on LG10 accounting for 15.5% of the phenotypic variation explanation (PVE) under well-watered conditions and a putative QTL for the same trait mapped on LG10 with reduced PVE (10.10%) under drought-stressed conditions in the F3 segregating population. Significant QTLs associated with number of seeds per plant, number of double-seeded pod per plant, seed weight per plant and pod weight per plant were mapped on LG4 (nearest marker: 4181663 and 4175954) with overlapping confidence intervals and explaining 21.9%, 21.8%, 23.5% and 19.9% of the PVE, respectively, under well-watered conditions in the F4 population, which could be considered as major QTL involved in the control of these traits. Fourteen QTL loci that were found to be consensus QTLs for yield-related, morphological and physiological traits across LG1A, LG2, LG3, LG4, LG5, LG7A, LG7B, LG10 and LG11. This study provides a pipeline for the development of breeding resources, including structured populations and breeding lines, for genetic analysis, trait dissection and potentially development of new improved varieties. The study also provides fundamental knowledge of QTLs associated with yield components, morphological and physiological traits under well-watered and drought-stressed conditions in bambara groundnut, which is also essential for yield improvement of bambara groundnut in response to drought stress

Benefits of laboratory personalized antiplatelet therapy in patients undergoing percutaneous coronary intervention: A meta-analysis of randomized controlled trials

   Background: The preventive effects of laboratory personalized antiplatelet therapy (PAPT) strategy in­cluding genetic detection and platelet function testing (PFT) on major adverse cardiac events (MACEs) and bleeding events in coronary artery disease (CAD) patients undergoing stenting has been extensively studied. Despite that, no clear conclusion can be drawn. In this study, a meta-analysis was performed to explore a more precise estimation of the benefits of laboratory PAPT. Methods: Randomized controlled trials were identified by the use of search databases such as PubMed, Embase, and Cochrane Controlled Trials Register up to May 2017, and the estimates were pooled. Results: Fourteen studies including 9497 patients met the inclusion criteria. The laboratory PAPT reduced MACEs risk (risk ratio [RR] 0.58, 95% confidence interval [CI] 0.42–0.80, p = 0.001), stent thrombosis (RR 0.60, 95% CI 0.41–0.87, p = 0.008) and myocardial infarctions (RR 0.43, 95% CI 0.21–0.88, p = 0.02) compared to the non-PAPT group. No statistically significant difference was observed between the two groups regarding cardiovascular death (RR 0.77, 95% CI 0.51–1.16, p = 0.21), bleeding events (RR 0.96, 95% CI 0.81–1.13, p = 0.59) and ischemic stroke (RR 0.81; 95% CI 0.39–1.66, p = 0.57). The preventive effect on MACEs was more significant in patients with high on-treatment platelet reactivity (RR 0.46; 95% CI 0.27–0.80, p = 0.006). Conclusions: Coronary artery disease patients after stenting could obtain benefits from laboratory PAPT. (Cardiol J 2018; 25, 1: 128–141

Deciphering the molecular basis for photosynthetic parameters in Bambara groundnut ( Vigna subterranea L. Verdc) under drought stress

Background: Assessment of segregating populations for their ability to withstand drought stress conditions is one of the best approaches to develop breeding lines and drought tolerant varieties. Bambara groundnut (Vigna subterranea L. Verdc.) is a leguminous crop, capable of growing in low-input agricultural systems in semi-arid areas. An F4 bi-parental segregating population obtained from S19-3 × DodR was developed to evaluate the effect of drought stress on photosynthetic parameters and identify QTLs associated with these traits under drought-stressed and well-watered conditions in a rainout shelter. Results: Stomatal conductance (gs), photosynthesis rate (A), transpiration rate (E) and intracellular CO2 (Ci) were significantly reduced (p < 0.05) while water use efficiency (WUE) was significantly increased (p < 0.05) under drought-stressed conditions. A strong linear correlation was observed between gs, WUE, A, E and Ci under both water regimes. The variability between different water treatment, among individual lines and the interaction between lines and environment for photosynthetic parameters provides resources for superior lines selection and drought resistant variety improvement. Significant QTL for gs and FV/FM under well-watered conditions were mapped on LG5 and LG3, respectively, with more than 20% of the PVE, which could be considered as the major QTL to control these traits. Five clustered QTLs for photosynthetic traits under drought-stressed and well-watered conditions were mapped on LG5, LG6A, LG10 and LG11, respectively. Conclusions: Significant and putative QTLs associated with photosynthetic parameters and the effect of drought stress on these traits have been revealed by QTL linkage mapping and field experiment in the F4 segregating population derived from S19-3 × DodR in bambara groundnut. The study provides fundamental knowledge of how photosynthetic traits response to drought stress and how genetic features control these traits under drought-stressed and well-watered conditions in bambara groundnut

Variation of phenotypic traits in twelve bambara groundnut (vigna subterranea (L.) Verdc.) genotypes and Two F2 Bi-Parental Segregating Populations

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). Underutilised species such as bambara groundnut (Vigna subterranea (L.) Verdc.) have the potential to contribute significantly to meeting food and nutritional needs worldwide. We evaluated phenotypic traits in twelve bambara groundnut genotypes from East, West and Southern Africa and Southeast Asia and two F2 bi-parental segregating populations derived from IITA-686 ×Tiga Nicuru and S19-3 ×DodR to determine phenotypic trait variation and their potential contribution to the development of improved crop varieties. All phenotypic traits in twelve genotypes were significantly influenced (p < 0.01) by genotypes. Principal component analysis (PCA) showed that PC1 accounted for 97.33% variation and was associated with four genotypes collected from East and Southern Africa. PC2 accounted for 2.48% of the variation and was associated with five genotypes collected from East, West and Southern Africa. Transgressive segregation for a number of traits was observed in the two F2 bi-parental populations, as some individual lines in the segregating populations showed trait values greater or less than their parents. The variability between twelve genotypes and the two F2 bi-parental segregating populations and the negative relationship between plant architectural traits and yield related traits provide resources for development of structured populations and breeding lines for bambara groundnut breeding programme

Transformation between phreatic water and soil water during freeze–thaw periods

During freeze–thaw periods, the exchange between shallow groundwater and soil water is unusually strong and bidirectional, which causes soil salinization and affects the accuracy of water resources assessment. The objectives of this study were to explore the laws of transformation between phreatic water and soil water through nine different groundwater table depths (GTDs) and three kinds of lithologies during three successive freeze–thaw periods using field lysimeters. The results showed that phreatic evaporation increased with smaller average soil particle sizes. The differences between phreatic evaporation and recharge to groundwater (DPR) and GTDs were well fitted by the semi-logarithmic model, and the regression coefficients A and B of the model were well fitted by the linear relationship with the average soil particle size. With the increase of soil particle size, the change of DPR decreased with the change rate of soil particle size. The extent of transformation between phreatic water and soil water decreased with the increase of soil particle size. During the whole freeze–thaw period, the negative value of DPR increased with an decrease in GTD. The groundwater depths of zero DPR (D-zero) of sandy loam, fine sand and sandy soil during the freeze–thaw periods were 2.79 m, 2.21 m and 2.12 m, respectively. This research is significant for the prevention of soil salinization disasters and the accurate assessment of water resources

Germline-Encoded TCR-MHC Contacts Promote TCR V Gene Bias in Umbilical Cord Blood T Cell Repertoire.

T cells recognize antigens as peptides bound to major histocompatibility complex (MHC) proteins through T cell receptors (TCRs) on their surface. To recognize a wide range of pathogens, each individual possesses a substantial number of TCRs with an extremely high degree of variability. It remains controversial whether germline-encoded TCR repertoire is shaped by MHC polymorphism and, if so, what is the preference between MHC genetic variants and TCR V gene compatibility. To investigate the "net" genetic association between MHC variations and TRBV genes, we applied quantitative trait locus (QTL) mapping to test the associations between MHC polymorphism and TCR β chain V (TRBV) genes usage using umbilical cord blood (UCB) samples of 201 Chinese newborns. We found TRBV gene and MHC loci that are predisposed to interact with one another differ from previous conclusions. The majority of MHC amino acid residues associated with the TRBV gene usage show spatial proximities in known structures of TCR-pMHC complexes. These results show for the first time that MHC variants bias TRBV gene usage in UCB of Chinese ancestry and indicate that germline-encoded contacts influence TCR-MHC interactions in intact T cell repertoires

Exome Sequencing Identifies Genetic Variants Associated with Circulating Lipid Levels in Mexican Americans: The Insulin Resistance Atherosclerosis Family Study (IRASFS)

Genome-wide association studies have identified numerous variants associated with lipid levels; yet, the majority are located in non-coding regions with unclear mechanisms. In the Insulin Resistance Atherosclerosis Family Study (IRASFS), heritability estimates suggest a strong genetic basis: low-density lipoprotein (LDL, h2 = 0.50), high-density lipoprotein (HDL, h2 = 0.57), total cholesterol (TC, h2 = 0.53), and triglyceride (TG, h2 = 0.42) levels. Exome sequencing of 1,205 Mexican Americans (90 pedigrees) from the IRASFS identified 548,889 variants and association and linkage analyses with lipid levels were performed. One genome-wide significant signal was detected in APOA5 with TG (rs651821, PTG = 3.67 × 10−10, LODTG = 2.36, MAF = 14.2%). In addition, two correlated SNPs (r2 = 1.0) rs189547099 (PTG = 6.31 × 10−08, LODTG = 3.13, MAF = 0.50%) and chr4:157997598 (PTG = 6.31 × 10−08, LODTG = 3.13, MAF = 0.50%) reached exome-wide significance (P \u3c 9.11 × 10−08). rs189547099 is an intronic SNP in FNIP2 and SNP chr4:157997598 is intronic in GLRB. Linkage analysis revealed 46 SNPs with a LOD \u3e 3 with the strongest signal at rs1141070 (LODLDL = 4.30, PLDL = 0.33, MAF = 21.6%) in DFFB. A total of 53 nominally associated variants (P \u3c 5.00 × 10−05, MAF ≥ 1.0%) were selected for replication in six Mexican-American cohorts (N = 3,280). The strongest signal observed was a synonymous variant (rs1160983, PLDL = 4.44 × 10−17, MAF = 2.7%) in TOMM40. Beyond primary findings, previously reported lipid loci were fine-mapped using exome sequencing in IRASFS. These results support that exome sequencing complements and extends insights into the genetics of lipid levels

Comparison of Gene Expression and Genome-Wide DNA Methylation Profiling between Phenotypically Normal Cloned Pigs and Conventionally Bred Controls

Animal breeding via Somatic Cell Nuclear Transfer (SCNT) has enormous potential in agriculture and biomedicine. However, concerns about whether SCNT animals are as healthy or epigenetically normal as conventionally bred ones are raised as the efficiency of cloning by SCNT is much lower than natural breeding or In-vitro fertilization (IVF). Thus, we have conducted a genome-wide gene expression and DNA methylation profiling between phenotypically normal cloned pigs and control pigs in two tissues (muscle and liver), using Affymetrix Porcine expression array as well as modified methylation-specific digital karyotyping (MMSDK) and Solexa sequencing technology. Typical tissue-specific differences with respect to both gene expression and DNA methylation were observed in muscle and liver from cloned as well as control pigs. Gene expression profiles were highly similar between cloned pigs and controls, though a small set of genes showed altered expression. Cloned pigs presented a more different pattern of DNA methylation in unique sequences in both tissues. Especially a small set of genomic sites had different DNA methylation status with a trend towards slightly increased methylation levels in cloned pigs. Molecular network analysis of the genes that contained such differential methylation loci revealed a significant network related to tissue development. In conclusion, our study showed that phenotypically normal cloned pigs were highly similar with normal breeding pigs in their gene expression, but moderate alteration in DNA methylation aspects still exists, especially in certain unique genomic regions