Broad Genetic Diversity Research Articles

Genetic basis for lentil adaptation to summer cropping in northern temperate environments.

The continued success of lentil (Lens culinaris Medik.) genetic improvement relies on the availability of broad genetic diversity, and new alleles need to be identified and incorporated into the cultivated gene pool. Availability of robust and predictive markers greatly enhances the precise transfer of genomic regions from unadapted germplasm. Quantitative trait loci (QTL) for key phenological traits in lentil were located using a recombinant inbreed line (RIL) population derived from a cross between an Ethiopian landrace (ILL 1704) and a northern temperate cultivar (CDC Robin). Field experiments were conducted at Sutherland research farm in Saskatoon and at Rosthern, Saskatchewan, Canada during 2018 and 2019. A linkage map was constructed using 21,634 single nucleotide polymorphisms (SNPs) located on seven linkage groups (LGs), which correspond to the seven haploid chromosomes of lentil. Eight QTL were identified for six phenological traits. Flowering-related QTL were identified at two regions on LG6. FLOWERING LOCUS T (FT) genes were annotated within the flowering time QTL interval based on the lentil reference genome. Similarly, a major QTL for postflowering developmental processes was located on LG5 with several senescence-associated genes annotated within the QTL interval. The flowering time QTL was validated in a different genetic background indicating the potential use of the identified markers for marker-assisted selection to precisely transfer genomic regions from exotic germplasm into elite crop cultivars without disrupting adaptation.

The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm

Mangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi’s genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.

Detection of a novel species A, DS-1-like, G4P[6] rotavirus strain from a Brazilian child with gastroenteritis.

Rotaviruses belonging to species A (RVA) remain among the most common causes of severe gastroenteritis in children aged <5 years, leading to substantial morbidity and mortality worldwide. Genome reassortment events between two human strains or human and animal strains represent one of the mechanisms which appear to generate the broad genetic variability of circulating. According to a nucleotide, sequence-based classification system, RVA strains are currently classified into three genotype constellations includingWa-like (genogroup I), DS-1-like (genogroup II), and AU-like (genogroup III). The present study reports the detection of an unusual RVA G4P[6] strain (coded as strain HSE005),which might have originated from a natural reassortment event between human and animal RVA strains. Molecular characterization of this isolate showed that it belonged to genogroup II, genotype G4P[6]. In addition, two genes (VP3 and NSP4) of this strain denoted evidence of reassortment events involving strains of distinct zoonotic evolutionary origins. Therefore, we propose that a new G4P[6] strain was identified, highlighting a possible first zoonotic transmission including a reassortment event that involved the VP3 gene.

Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

The current assembled maize genomes cannot represent the broad genetic diversity of maize germplasms. Acquiring more genome sequences is critical for constructing a pan-genome and elucidating the linkage between genotype and phenotype in maize. Here we describe the genome sequence and annotation of A188, a maize inbred line with high phenotypic variation relative to other lines, acquired by single-molecule sequencing and optical genome mapping. We assembled a 2210-Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to 9.73 Mb for B73 and 10.2 Mb for Mo17. Based on the B73_RefGen_V4 genome, 295 scaffolds (2084.35 Mb, 94.30% of the final genome assembly) were anchored and oriented on ten chromosomes. Comparative analysis revealed that ~30% of the predicted A188 genes showed large structural divergence from B73, Mo17, and W22 genomes, which causes high protein divergence and may lead to phenotypic variation among the four inbred lines. As a line with high embryonic callus (EC) induction capacity, A188 provides a convenient tool for elucidating the molecular mechanism underlying the formation of EC in maize. Combining our new A188 genome with previously reported QTL and RNA sequencing data revealed eight genes with large structural variation and two differentially expressed genes playing potential roles in maize EC induction.

Hereditary spastic paraplegia: new insights into clinical variability and spasticity-ataxia phenotype, and novel mutations.

Hereditary spastic paraplegias (HSPs), a genetically heterogeneous group of neurodegenerative diseases, have an incidence of around 3 to 9 individuals every 100,000. Due to the broad clinical and genetic variability of HSPs, it is challenging to diagnose the disorder quickly and precisely. Hereditary spastic ataxias (HSAs) and HSPs are overlapping diseases, and their intersection has been gradually identified by next-generation sequencing. The idea of the spasticity-ataxia phenotype (SAP) spectrum is further substantiated by the similarities in phenotypes and underlying genes in ataxias and inherited spastic paraplegias and the related cellular processes and disease mechanisms these disorders exhibit. Whole-exome sequencing was performed on the 25 spastic or spastic-ataxic gait patients. Twenty-two specific HSPs-HSAs-SAP mutations, including 14 novel mutations, were found in 25 cases from 18 Turkish and 2 Syrian families. This research discovers many novel hereditary spastic paraplegia (HSP) mutations and shows a robust genotype-phenotype heterogeneity in the disease. This research helped expand the clinical and molecular scope of HSP and clarified the concept of the spasticity-ataxia phenotype, further enhancing our understanding of the complicated form of HSP and its association with ataxia. Our data broadens the spectrum of HSPs and HSAs related gene mutations and provides insights for genotype-phenotype correlations for HSPs and HSAs.

Morphological Characterization of Southern Jalisco, Mexico, Pomegranate Genotypes Using AFLP Markers

Pomegranate is gaining popularity because of its proved nutraceutical properties and is highly adaptable to different climates. In southern Jalisco, Mexico, 18 genotypes were characterized on the basis of fruit characteristics (21 traits) and AFLP (Amplified Fragment length polymorphism) markers. The first three components of a principal components analysis (PCA) explained 71.5% of the variation. The most important variables were related to fruit size and weight. Fruit weight, equatorial diameter, polar diameter, and rind and membrane weight were the variables that most contributed to principal component one (PC1) 46.4%. The variables juice per fruit, edible proportion, proportion of rind and membrane, and seed length contributed most to principal component two (PC2) 15.2%, while juice pH, weight of one seed, and aril width contributed the most to principal component three (PC3) 9.9%. With the six combinations of AFLP primers, 315 fragments were obtained (an average of 52.5 fragments per primer); of these, 229 were polymorphic (72.7% polymorphism). Grouping by both morphological traits and AFLP markers separated all the evaluated individuals so that there were no repeated genotypes. In both analyses, the grouping did not obey geographic origin of the genotypes (r = −0.35), suggesting that both techniques were useful and complementary in the characterization of pomegranate genotypes. The commercial cultivars Wonderful and Apaseo had low levels of similarity to genotypes from southern Jalisco. The level of polymorphism found and compared with the results obtained by other authors suggests that the pomegranate genotypes evaluated are highly polymorphic. We found broad genetic diversity that can be used in breeding programs.

Genomic Prediction of Resistance to Tar Spot Complex of Maize in Multiple Populations Using Genotyping-by-Sequencing SNPs.

Tar spot complex (TSC) is one of the most important foliar diseases in tropical maize. TSC resistance could be furtherly improved by implementing marker-assisted selection (MAS) and genomic selection (GS) individually, or by implementing them stepwise. Implementation of GS requires a profound understanding of factors affecting genomic prediction accuracy. In the present study, an association-mapping panel and three doubled haploid populations, genotyped with genotyping-by-sequencing, were used to estimate the effectiveness of GS for improving TSC resistance. When the training and prediction sets were independent, moderate-to-high prediction accuracies were achieved across populations by using the training sets with broader genetic diversity, or in pairwise populations having closer genetic relationships. A collection of inbred lines with broader genetic diversity could be used as a permanent training set for TSC improvement, which can be updated by adding more phenotyped lines having closer genetic relationships with the prediction set. The prediction accuracies estimated with a few significantly associated SNPs were moderate-to-high, and continuously increased as more significantly associated SNPs were included. It confirmed that TSC resistance could be furtherly improved by implementing GS for selecting multiple stable genomic regions simultaneously, or by implementing MAS and GS stepwise. The factors of marker density, marker quality, and heterozygosity rate of samples had minor effects on the estimation of the genomic prediction accuracy. The training set size, the genetic relationship between training and prediction sets, phenotypic and genotypic diversity of the training sets, and incorporating known trait-marker associations played more important roles in improving prediction accuracy. The result of the present study provides insight into less complex trait improvement via GS in maize.

Phenotypic Characterization of Quinoa (Chenopodium quinoa Willd.) for the Selection of Promising Materials for Breeding Programs.

Quinoa is an ancestral crop in the Andean region, characterized by its adaptability to different agroclimatic conditions, great nutritional value, and broad genetic variability. A preliminary approach for understanding the genetics of quinoa materials entails a morphologic characterization, which can provide the basis for the selection of materials that satisfy the needs of farmers and consumers. Therefore, this study aimed to evaluate the phenotypic characteristics of thirty genetic C. quinoa accessions for the selection of outstanding accessions in terms of yield and grain quality. A randomized complete block design was used, with nine replications for each accession under greenhouse conditions. Nine quantitative and twelve qualitative descriptors were evaluated with descriptive analysis, Spearman correlation variance, and multivariate and cluster analysis. The results showed that the accessions with heights greater than the average (>176.72 cm) and long panicles (>57.94 cm) presented lower yields and smaller seed sizes, thus decreasing the grain quality. The multivariate and cluster analyses established groups of accessions with good yields (>62.02 g of seeds per plant) and stable morphological characteristics. The proposed selection index, based on yield components and morphological descriptors, indicated four accessions as potential parents for quinoa breeding programs in Colombia.

Grass and legume breeding matching the future needs of European grassland farming

AbstractPlant breeding can be pivotal to produce new grassland varieties with better adaptation to changes in seasonal pattern and increased variability of temperature, precipitation and length of the growing seasons as determined by climate change. Cultivation of legume species is expected to increase, and will make crop–livestock systems more sustainable and self‐sufficient for feed proteins. In northern Europe, the higher temperatures and longer growing season will create opportunities for increasing yield, while in southern Europe greater drought tolerance and growth in the cool seasons will be indispensable to maintain crop yields. Greater intra‐ and interspecific diversity is recommended for grasslands in both regions. In the north, also broader genetic diversity, particularly in terms of adaptation pattern (response diversity), is needed, requiring pre‐breeding to enlarge the gene pool by introgression of exotic, less adapted genetic resources as a first step. Genetic gain in forage crop breeding has been modest over time, and new breeding methods need to be implemented to speed up the development of new cultivars with proper adaptation to future climate conditions. Novel technologies such as genome‐enabled selection and high‐throughput phenotyping will play a major role in this context. They are rapidly evolving and increasingly adopted, albeit with technical challenges and a need for optimization of breeding schemes for optimal exploitation.

Genetic Diversity Assessment of MPOB-Senegal Oil Palm Germplasm Using Microsatellite Markers.

Molecular characterization of oil palm germplasm is crucial in utilizing and conserving germplasm with promising traits. This study was conducted to evaluate the genetic diversity structures and relationships among 26 families of MPOB-Senegal oil palm germplasm using thirty-five microsatellite markers. High level of polymorphism (P = 96.26%), number of effective allele (Ne = 2.653), observed heterozygosity (Ho = 0.584), expected heterozygosity (He = 0.550), total heterozygosity (HT = 0.666), and rare alleles (54) were observed which indicates that MPOB-Senegal germplasm has a broad genetic variation. Among the SSR markers, sMo00053 and sMg00133 were the most informative markers for discrimination among the MPOB-Senegal oil palm germplasm for having the highest private alleles and the rare alleles. For selection and conservation, oil palm populations with high rare alleles and Nei's gene diversity index should be considered as these populations may possess unique genes for further exploitation.

Assessment of Genetic Diversity in Various Yield Traits to Determine a High Yielding New Type of Upland Rice

This experiment's objective was to estimate the genetic diversity of F5 populations on various yield components for developing high-yielding upland rice. The experiment was carried out from April to August 2018 at Semarang Village, Bengkulu, Indonesia. Plant materials used in the experiment were 160 accessions of F4, obtained from a pedigree selection of crossing between two local landraces (Sriwijaya and Bugis) and two introduced accessions (IR-148 and IR-7858-1). The experiment was arranged in Augmented Design with a spaced planting system (20 x 20 cm). The variance between populations was determined by Principal Component Analysis (PCA) with XLSTAT version 9.0. Broad sense genetic diversity was found for the number of traits, such as number of panicles, the total number of grains per panicle, number of empty grains per panicle, number of filled grain per panicle, percentage of empty grain, the weight of 1000 grains, the weight of grain per hill, which potentially improved high yielding. These genotypes were categorized into three groups. Group I showed superior traits for the total number of grains per panicle, the number of filled grain per panicle, weight of 1000 grains, and weight of grain per hill found in genotypes BKL4-B-2, BKL3-B-3, BKL4-B-3, BKL3-B-2. Group II had superior traits for panicle length, the number of empty grains per panicle, and the percentage of empty grain were BKL1-RS*1-3, BKL1-RS*1-1, BKL3-RS*1-1, BKL3-RS*1-3, BKL1-RS*1-2, BKL2-RS*1-2, and BKL2-RS*1-1. Groups III was superior to the number of panicle traits found in genotypes BKL2-B-2, BKL3-B-1, BKL1-B-1, BKL1-B-2, and BKL2-B-1.

Molecular characterization of vancomycin-resistant Enterococcus faecium isolates from two German hospitals.

Introduction: Vancomycin-resistant Enterococcus faecium accounts for around 10–23% of nosocomial enterococcal infections and constitutes a relevant therapeutic problem due to its limited susceptibility to antibiotics. The resistance towards glycopeptide antibiotics is mediated by the so-called van genes. Currently, the most common resistance type in Germany is the vanB-type. Little data are available on the molecular epidemiology in Germany. Therefore, an epidemiological typing of Enterococcus faecium isolates with vanB-type resistance from two German hospitals in Essen and Nuremberg was performed. Two outbreaks and 104 sporadic cases were investigated. Methods: All 128 isolates with vanB-type resistance were collected between 2011–2012 and 2017–2018. They were characterized using multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Results: ST 117 was the most common sequence type (ST) in both hospitals, especially since 2017. PFGE divided the isolates of this study into 68 PFGE types and showed a broad genetic diversity. Two epidemiologically assumed in-hospital outbreaks were genetically confirmed. Apart from that, in-hospital transmissions were rare events. Conclusion: The results obtained by MLST confirmed the previously described allocation of STs in Germany. PFGE showed a broad genetic diversity of vanB VRE between the two hospitals and also within each hospital. In-hospital transmissions were rare, but outbreaks did occur. Our data supports the strategy to screen and isolate patients in transmission events in order to detect monoclonality indicating a common source or hygiene mismanagement.

Physiological and pollen-based screening of shrub roses for hot and drought environments

Rose plants growing under natural conditions are exposed to unfavorable environmental conditions such as high temperature and drought, particularly around the blooming stage. This can reduce the reproductive potential and aesthetic value of commercial rose cultivars, which are often more sensitive to harsh conditions. Plants adjust to adverse environments by regulating several morpho-physiological and biochemical processes, which are the key to tolerance mechanisms. Thus, to examine genetic potential of 22 roses, we characterized 18 traits: gas exchange, leaf biophysical, pigments, and pollen germination characteristics using field-grown roses at the blooming stage. A broad genetic variability (P < 0.001) in all measured traits suggests that roses comprise heat- and drought-adaptive traits. A weak correlation between the pollen viability or germination and the pollen tube length at 38 °C signifying the complexity of reproductive processes. However, three rose cultivars, Moje Hammarberg, Carefree Spirit, and Lavender Meidiland had better pollen germination-related traits (25 %) along with high photosynthetic capacity (24 %) and pigment traits (22 %) compared with sensitive cultivars. The generated phenotypic data, along with reliable phenotyping methods and identified candidate cultivars, would help develop roses with enhanced resilience to stress for dry and hotter climates.

Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus

BackgroundMicrococcus luteus is a group of actinobacteria that is widely used in biotechnology and is being thought as an emerging nosocomial pathogen. With one of the smallest genomes of free-living actinobacteria, it is found in a wide range of environments, but intraspecies genetic diversity and adaptation strategies to various environments remain unclear. Here, comparative genomics, phylogenomics, and genome-wide association studies were used to investigate the genomic diversity, evolutionary history, and the potential ecological differentiation of the species.ResultsHigh-quality genomes of 66 M. luteus strains were downloaded from the NCBI GenBank database and core and pan-genome analysis revealed a considerable intraspecies heterogeneity. Phylogenomic analysis, gene content comparison, and average nucleotide identity calculation consistently indicated that the species has diverged into three well-differentiated clades. Population structure analysis further suggested the existence of an unknown ancestor or the fourth, yet unsampled, clade. Reconstruction of gene gain/loss events along the evolutionary history revealed both early events that contributed to the inter-clade divergence and recent events leading to the intra-clade diversity. We also found convincing evidence that recombination has played a key role in the evolutionary process of the species, with upto two-thirds of the core genes having been affected by recombination. Furthermore, distribution of mammal-associated strains (including pathogens) on the phylogenetic tree suggested that the last common ancestor had a free-living lifestyle, and a few recently diverged lineages have developed a mammal-associated lifestyle separately. Consistently, genome-wide association analysis revealed that mammal-associated strains from different lineages shared genes functionally relevant to the host-associated lifestyle, indicating a recent ecological adaption to the new host-associated habitats.ConclusionsThese results revealed high intraspecies genomic diversity of M. luteus and highlighted that gene gain/loss events and extensive recombination events played key roles in the genome evolution. Our study also indicated that, as a free-living species, some lineages have recently developed or are developing a mammal-associated lifestyle. This study provides insights into the mechanisms that drive the genome evolution and adaption to various environments of a bacterial species.

Genetic Architecture and Genomic Prediction of Cooking Time in Common Bean (Phaseolus vulgaris L.).

Cooking time of the common bean is an important trait for consumer preference, with implications for nutrition, health, and environment. For efficient germplasm improvement, breeders need more information on the genetics to identify fast cooking sources with good agronomic properties and molecular breeding tools. In this study, we investigated a broad genetic variation among tropical germplasm from both Andean and Mesoamerican genepools. Four populations were evaluated for cooking time (CKT), water absorption capacity (WAC), and seed weight (SdW): a bi-parental RIL population (DxG), an eight-parental Mesoamerican MAGIC population, an Andean (VEF), and a Mesoamerican (MIP) breeding line panel. A total of 922 lines were evaluated in this study. Significant genetic variation was found in all populations with high heritabilities, ranging from 0.64 to 0.89 for CKT. CKT was related to the color of the seed coat, with the white colored seeds being the ones that cooked the fastest. Marker trait associations were investigated by QTL analysis and GWAS, resulting in the identification of 10 QTL. In populations with Andean germplasm, an inverse correlation of CKT and WAC, and also a QTL on Pv03 that inversely controls CKT and WAC (CKT3.2/WAC3.1) were observed. WAC7.1 was found in both Mesoamerican populations. QTL only explained a small part of the variance, and phenotypic distributions support a more quantitative mode of inheritance. For this reason, we evaluated how genomic prediction (GP) models can capture the genetic variation. GP accuracies for CKT varied, ranging from good results for the MAGIC population (0.55) to lower accuracies in the MIP panel (0.22). The phenotypic characterization of parental material will allow for the cooking time trait to be implemented in the active germplasm improvement programs. Molecular breeding tools can be developed to employ marker-assisted selection or genomic selection, which looks to be a promising tool in some populations to increase the efficiency of breeding activities.

Genome-wide association mapping identifies HvNIP2;2/HvLsi6 accounting for efficient boron transport in barley.

Boron (B) is an essential mineral element for plant growth, and the seed B pool of crops can be crucial when seedlings need to establish on low-B soils. To date, it is poorly understood how B accumulation in grain crops is genetically controlled. Here, we assessed the genotypic variation of the B concentration in grains of a spring barley (Hordeum vulgare L.) association panel that represents broad genetic diversity. We found a large genetic variation of the grain B concentration and detected in total 23 quantitative trait loci (QTLs) using genome-wide association mapping. HvNIP2;2/HvLsi6, encoding a potential B-transporting membrane protein, mapped closely to a major-effect QTL accounting for the largest proportion of grain B variation. Based on transport studies using heterologous expression systems and gene expression analysis, we demonstrate that HvNIP2;2/HvLsi6 represents a functional B channel and that expression variation in its transcript level associates with root and shoot B concentrations as well as with root dry mass formation under B-deficient conditions.

Molecular Characterization of Thirteen Oil seed Brassica L. Variants From Bangladesh Through Polyacrylamide Gel Electrophoresis (PAGE)

Brassica L. is the most agronomical important genus of Brassicaceae family. An electrophoretic exploration was conveyed for proper identification of genetically diverse and agronomically superior genotypes and pursuing the extent of genetic divergence and phylogenetic relationship within the thirteen variants of Brassica for leaf storage protein by using Polyacrylamide Gel Electrophoresis (PAGE) as biochemical marker. A total of 19 alternative protein bands were found with high polymorphism of 89.47%. The protein banding pattern suggested the existence of differences among the studied variants pertaining to the location, molecular weight and staining intensity of the bands which could be utilized as fingerprints for variants identification. Based on Nei’s genetic distance, a wide range of genetic distance (0.0541–1.5581) offered the presence of broad genetic variability among the quested variants. A dendrogram was constructed by using UPGMA where all the analyzed Brassica variants were rouped into two major clusters. Relying on this analysis, highest genetic variation (1.5581) was observed between BS-10 and BS-14 while the lowest genetic variation (0.0541) was recorded between BS-9 and BS-12, which might be furnished as a source of parental line. Consequently, it can be proposed that the protein profile of the analyzed thirteen variants of Brassica L. by PAGE would be considered to be a contributory implement to the breeders of Brassica by providing sufficient information on the genetic resources of Brassica and improvement of new offspring in the forthcoming breeding program of Brassica L.

Genetic characterization of popcorn hybrids based on SNP genotyping and development of rapid ARMS based primers

In South Korea, popcorn consumption may have boomed in recent years but little has changed little for farmers or breeders. The majority of popcorn sold in the domestic market is derived from imported hybrids. The efforts are needed to identify parental lines and develop hybrids suitable for domestic conditions. However, the major constraint remains a narrow germplasm pool. Thus, knowledge of genetic variability among germplasm as well as among commercial hybrids is important to avoid genetic uniformity, thereby reducing the risk of vulnerability to stress and yield loss. Recently, the Maize Research Institute in Hongcheon developed valuable breeding material: ‘G-popcorn’, a new hybrid, together with ‘Oryun popcorn’, ‘Oryun popcorn2′, and ‘Gichan popcorn’. In this study, we assessed the genetic relationships among domestic and imported hybrids using 55 k single-nucleotide polymorphism (SNP) markers. Approximately 80% of the SNP markers were highly informative for future routine and low-cost genotyping. Considerable polymorphism among the SNP markers was observed with regard to reproducibility, ease of scoring, and minor allele frequency. Broad genetic diversity was detected among the germplasm analyzed; cluster analysis revealed the presence of two distinct groups of hybrids and generally agreed with pedigree information. In addition, we demonstrated the conversion of bead-chip SNP alleles into species-specific primers and used the ARMS-PCR technique to differentiate imported and domestic popcorn hybrids. The developed method will be useful for rapid and cost-effective identification of genetic purity among popcorn hybrids.

Determination of Genetic Parameters of Seed Characteristics in Edible Soybean

Background: Knowledge about genetic parameters can help plant breeders to determine which selection criteria are beneficial. This study aims to estimate the genetic parameters of soybean seed characteristics.Methods: A total of 91 soybean lines from three different populations were evaluated during dry season in 2016. All genetic material used was grown following a randomized complete block design with two replicates. Soybean pods were harvested after 90% of the leaves had yellowed or fallen. The characteristics of the seeds observed included length, width, thickness and weight of 100 seeds.Result: The results showed that there were two seed shapes (round and ellipse) and two seed sizes (large and medium). There is a broad genetic variability of soybean seed characteristics. Heritability broad sense varies from 0.42 to 0.84, classified as moderate (length-width ratio) to high (length, width, thickness, length-thickness ratio, width-thickness ration and weight of 100 seeds). This therefore shows that there is an opportunity to improve the characters of soybean seeds. The length, width, thickness, ratio of the three characters and the weight of 100 seeds can be used as selection criteria in a soybean breeding program to obtain large-seeded soybeans with a round or elliptical shape.

Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host.

Plasmids are autonomously replicating sequences that help cells adapt to diverse stresses. Theta plasmids are the most frequent plasmid class in enterobacteria. They co-opt two host replication mechanisms: replication at oriC, a DnaA-dependent pathway leading to replisome assembly (theta class A), and replication fork restart, a PriA-dependent pathway leading to primosome assembly through primer extension and D-loop formation (theta classes B, C, and D). To ensure autonomy from the host's replication and to facilitate copy number regulation, theta plasmids have unique mechanisms of replication initiation at the plasmid origin of replication (ori). Tight plasmid copy number regulation is essential because of the major and direct impact plasmid gene dosage has on gene expression. The timing of plasmid replication and segregation are also critical for optimizing plasmid gene expression. Therefore, we propose that plasmid replication needs to be understood in its biological context, where complex origins of replication (redundant origins, mosaic and cointegrated replicons), plasmid segregation, and toxin-antitoxin systems are often present. Highlighting their tight functional integration with ori function, we show that both partition and toxin-antitoxin systems tend to be encoded in close physical proximity to the ori in a large collection of Escherichia coli plasmids. We also propose that adaptation of plasmids to their host optimizes their contribution to the host's fitness while restricting access to broad genetic diversity, and we argue that this trade-off between adaptation to host and access to genetic diversity is likely a determinant factor shaping the distribution of replicons in populations of enterobacteria.