Molecular marker applications in plants

Genetic diversity and population structure analysis of 418 tomato cultivars based on single nucleotide polymorphism markers

Introduction

Tomato (Solanum lycopersicum) is a highly valuable fruit crop. However, due to the lack of scientific and accurate variety identification methods and unified national standards, production management is scattered and non-standard, resulting in mixed varieties. This poses considerable difficulties for the cataloging and preservation of germplasm resources as well as the identification, promotion, and application of new tomato varieties.

Methods

To better understand the genetic diversity and population structure of representative tomato varieties, we collected 418 tomato varieties from the past 20 years and analyzed them using genome-wide single nucleotide polymorphism (SNP) markers. We initially assessed the population structure, genetic relationships, and genetic profiles of the 418 tomato germplasm resources utilizing simplified genome sequencing techniques. A total of 3,374,929 filtered SNPs were obtained and distributed across 12 chromosomes. Based on these SNP loci, the 418 tomatoes samples were divided into six subgroups.

Results

The population structure and genetic relationships among existing tomato germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Rigorous selection criteria identified 15 additional high-quality DNA fingerprints from 50 validated SNP loci, effectively enabling the identification of the 418 tomato varieties, which were successfully converted into KASP (Kompetitive Allele Specific PCR) markers.

Discussion

This study represents the first comprehensive investigation assessing the diversity and population structure of a large collection of tomato varieties. Overall, it marks a considerable advancement in understanding the genetic makeup of tomato populations. The results broadened our understanding of the diversity, phylogeny, and population structure of tomato germplasm resources. Furthermore, this study provides a scientific basis and reference data for future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding in tomatoes.

Genome Sequencing of Lentinula edodes Revealed a Genomic Variant Block Associated with a Thermo-Tolerant Trait in Fruit Body Formation

The formation of multicellular fruiting bodies in basidiomycete mushrooms is a crucial developmental process for sexual reproduction and subsequent spore development. Temperature is one of the most critical factors influencing the phase transition for mushroom reproduction. During the domestication of mushrooms, traits related to fruiting bodies have significantly impacted agricultural adaptation and human preferences. Recent research has demonstrated that chromosomal variations, such as structural variants (SVs) and variant blocks (VBs), play crucial roles in agronomic traits and evolutionary processes. However, the lack of high-quality genomic information and important trait data have hindered comprehensive identification and characterization in Lentinula edodes breeding processes. In this study, the genomes of two monokaryotic L. edodes strains, characterized by thermo-tolerance and thermo-sensitivity during fruiting body formation, were reassembled at the chromosomal level. Comparative genomic studies of four thermo-tolerant and thermo-sensitive monokaryotic L. edodes strains identified a 0.56 Mbp variant block on chromosome 9. Genes associated with DNA repair or cellular response to DNA damage stimulus were enriched in this variant block. Finally, we developed eight CAPS markers from the variant block to discriminate the thermo-tolerant traits in L. edodes cultivars. Our findings show that the identified variant block is highly correlated with the thermo-tolerant trait for fruiting body formation and that alleles present in this block may have been artificially selected during L. edodes domestication.

MegaSSR: a web server for large scale microsatellite identification, classification, and marker development

Next-generation sequencing technologies have opened new avenues for using genomic data to study and develop molecular markers and improve genetic resources. Simple Sequence Repeats (SSRs) as genetic markers are increasingly used in molecular diversity and molecular breeding programs that require bioinformatics pipelines to analyze the large amounts of data. Therefore, there is an ongoing need for online tools that provide computational resources with minimal effort and maximum efficiency, including automated development of SSR markers. These tools should be flexible, customizable, and able to handle the ever-increasing amount of genomic data. Here we introduce MegaSSR (https://bioinformatics.um6p.ma/MegaSSR), a web server and a standalone pipeline that enables the design of SSR markers in any target genome. MegaSSR allows users to design targeted PCR-based primers for their selected SSR repeats and includes multiple tools that initiate computational pipelines for SSR mining, classification, comparisons, PCR primer design, in silico PCR validation, and statistical visualization. MegaSSR results can be accessed, searched, downloaded, and visualized with user-friendly web-based tools. These tools provide graphs and tables showing various aspects of SSR markers and corresponding PCR primers. MegaSSR will accelerate ongoing research in plant species and assist breeding programs in their efforts to improve current genomic resources.

Comparative analysis indicates a simple protocol for DNA extraction of the aromatic plant Lippia alba

An efficient method of genomic DNA extraction that provides high quality and yield is a crucial pre-requisite and limiting factor in plant genetic analysis. However, pure genomic DNA can be challenging to obtain from some plant species due to their sugar and secondary metabolite contents. Lippia alba is an important aromatic and medicinal plant, chemically characterized by the presence of tannins, flavonoids, anthocyanins, and essential oils, which interfere with the extraction of pure genomic DNA. In this scenario, optimizing the extraction methods and minimizing the effects of these compounds are necessary. This study compares six plant DNA extraction protocols based on the CTAB method. The quality and quantity of DNA samples obtained were determined by physical appearance by electrophoresis in agarose gels and spectrophotometry. The results highlight the difficulty in obtaining pure and clear bands for all tested methods, except for the polyvinylpyrrolidone (PVP)-based protocol created by our team, which was the better option for obtaining high-quality genomic DNA of L. alba. We conclude that adding PVP-40 into DNA extraction buffers can optimize the DNA extraction of L. alba and indicate this protocol for DNA extraction from other aromatic plants.

Construction of SNP fingerprint and population genetic analysis of honeysuckle germplasm resources in China

INTRODUCTION

The flower buds of Lonicera japonica Thunb. are widely used in Chinese medicine for their anti-inflammatory properties, and they have played an important role in the fight against SARS COVID-19 and other major epidemics. However, due to the lack of scientific and accurate variety identification methods and national unified standards, scattered and non-standardized management in flower bud production has led to mixed varieties that have caused significant difficulties in the cataloging and preservation of germplasm resources and the identification, promotion, and application of new L. japonica varieties.

METHODS

In this study, we evaluated the population structure, genetic relationships, and genetic fingerprints of 39 germplasm resources of Lonicera in China using simplified genome sequencing technology.

RESULTS

A total of 13,143,268 single nucleotide polymorphisms (SNPs) were identified. Thirty-nine samples of Lonicera were divided into four subgroups, and the population structure and genetic relationships among existing Lonicera germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Through several stringent selection criteria, 15 additional streamlined, high-quality DNA fingerprints were filtered out of the validated 50 SNP loci and verified as being able to effectively identify the 39 Lonicera varieties.

DISCUSSION

To our knowledge, this is the first comprehensive study measuring the diversity and population structure of a large collection of Lonicera varieties in China. These results have greatly broadened our understanding of the diversity, phylogeny, and population structure of Lonicera. The results may enhance the future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding by providing a scientific basis and reference data for these efforts.

Cytogeography of Naturalized Solidago canadensis Populations in Europe

Autopolyploidization has driven the successful invasion of Solidago canadensis in East Asia. However, it was believed that only diploid S. canadensis invaded Europe, whereas polyploids never did. Here, molecular identification, ploidy level, and morphological traits of ten S. canadensis populations collected in Europe were compared with previously identified S. canadensis populations from other continents and S. altissima populations. Furthermore, the ploidy-driven geographical differentiation pattern of S. canadensis in different continents was investigated. All ten European populations were identified as S. canadensis with five diploid and five hexaploid populations. Significant differences in morphological traits existed among diploids and polyploids (tetraploids and hexaploids), rather than between polyploids from different introduced ranges and between S. altissima and polyploidy S. canadensis. The invasive hexaploids and diploids had few differences in latitudinal distributions in Europe, which was similar to the native range but different from a distinct climate-niche differentiation in Asia. This may be attributed to the bigger difference in climate between Asia and Europe and North America. The morphological and molecular evidences proved the invasion of polyploid S. canadensis in Europe and suggest that S. altissima may be merged into a complex of S. canadensis species. Our study may be concluded that geographical and ecological niche differentiation of an invasive plant driven by ploidy depends on the degree of difference in the environmental factors between the introduced and native range, which provides new insight into the invasive mechanism.

Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios

Genetic improvement of temperate fruit and nut crops through conventional breeding methods is not sufficient alone due to its extreme time-consuming, cost-intensive, and hard-to-handle approach. Again, few other constraints that are associated with these species, viz., their long juvenile period, high heterozygosity, sterility, presence of sexual incompatibility, polyploidy, etc., make their selection and improvement process more complicated. Therefore, to promote precise and accurate selection of plants based on their genotypes, supplement of advanced biotechnological tools, viz., molecular marker approaches along with traditional breeding methods, is highly required in these species. Different markers, especially the molecular ones, enable direct selection of genomic regions governing the trait of interest such as high quality, yield, and resistance to abiotic and biotic stresses instead of the trait itself, thus saving the overall time and space and helping screen fruit quality and other related desired traits at early stages. The availability of molecular markers like SNP (single-nucleotide polymorphism), DArT (Diversity Arrays Technology) markers, and dense molecular genetic maps in crop plants, including fruit and nut crops, led to a revelation of facts from genetic markers, thus assisting in precise line selection. This review highlighted several aspects of the molecular marker approach that opens up tremendous possibilities to reveal valuable information about genetic diversity and phylogeny to boost the efficacy of selection in temperate fruit crops through genome sequencing and thus cultivar improvement with respect to adaptability and biotic and abiotic stress resistance in temperate fruit and nut species.

Genetic diversity analysis and variety identification using SSR and SNP markers in melon

Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for variety evaluation, discrimination, as well as innovation in breeding. Recently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), two robust molecular markers, have been utilized as a rapid and reliable method for variety identification. To elucidate the genetic structure and diversity of melon varieties, we screened out 136 perfect SSRs and 164 perfect SNPs from the resequencing data of 149 accessions, including the most representative lines worldwide. This study established the DNA fingerprint of 259 widely-cultivated melon varieties in China using Target-seq technology. All melon varieties were classified into five subgruops, including ssp. agrestis, ssp. melo, muskmelon and two subgroups of foreign individuals. Compared with ssp. melo, the ssp. agrestis varieties might be exposed to a high risk of genetic erosion due to their extremely narrow genetic background. Increasing the gene exchange between ssp. melo and ssp. agrestis is therefore necessary in the breeding procedure. In addition, analysis of the DNA fingerprints of the 259 melon varieties showed a good linear correlation (R² = 0.9722) between the SSR genotyping and SNP genotyping methods in variety identification. The pedigree analysis based on the DNA fingerprint of 'Jingyu' and 'Jingmi' series melon varieties was consistent with their breeding history. Based on the SNP index analysis, ssp. agrestis had low gene exchange with ssp. melo in chromosome 4, 7, 10, 11and 12, two specific SNP loci were verified to distinguish ssp. agrestis and ssp. melon varieties. Finally, 23 SSRs and 40 SNPs were selected as the core sets of markers for application in variety identification, which could be efficiently applied to variety authentication, variety monitoring, as well as the protection of intellectual property rights in melon.

Whole Genome Sequencing and Morphological Trait-Based Evaluation of UPOV Option 2 for DUS Testing in Rice

To evaluate the application potential of high-density SNPs in rice distinctness, uniformity, and stability (DUS) testing, we screened 37,929 SNP loci distributed on 12 rice chromosomes based on whole-genome resequencing of 122 rice accessions. These SNP loci were used to analyze the DUS testing of rice varieties based on the correlation between the molecular and phenotypic distances of varieties according to UPOV option 2. The results showed that statistical algorithms and the number of phenotypic traits and SNP loci all affected the correlation between the molecular and phenotypic distances of rice varieties. Relative to the other nine algorithms, the Jaccard similarity algorithm had the highest correlation of 0.6587. Both the number of SNPs and the number of phenotypes had a ceiling effect on the correlation between the molecular and phenotypic distances of varieties, and the ceiling effect of the number of SNP loci was more obvious. To overcome the correlation bottleneck, we used the genome-wide prediction method to predict 30 phenotypic traits and found that the prediction accuracy of some traits, such as the basal sheath anthocyanin color, glume length, and intensity of the green color of the leaf blade, was very low. In combination with group comparison analysis, we found that the key to overcoming the ceiling effect of correlation was to improve the resolution of traits with low predictive values. In addition, we also performed distinctness testing on rice varieties by using the molecular distance and phenotypic distance, and we found that there were large differences between the two methods, indicating that UPOV option 2 alone cannot replace the traditional phenotypic DUS testing. However, genotype and phenotype analysis together can increase the efficiency of DUS testing.

Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing

Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.

Agro-morphological and genetic diversity studies in Rice (Oryza sativa L.) germplasm using microsatellite markers

BACKGROUND

Knowledge of the genetic diversity and population structure of germplasm collections is an important foundation for crop improvement. Rice production across a broad range of rice-growing environments results in a diverse array of local rice varieties. Many rice varieties have been lost as a result of biodiversity loss and are now grown in Pakistan.

METHODS AND RESULTS

To protect the biodiversity of rice varieties, an experiment was carried out to check the genetic and morphological variations between 8 exotic and 7 local rice genotypes, using 5 different SSR markers, i.e., RM3, RM259, RM341, RM520, and RM11943. The analysis of morphological and quality traits of rice observed significant variation across genotypes. The results revealed that genotype Irri-Pak attained the highest plant height and primary branch plant-1, while genotype Mushkan produced a higher number of productive tillers and obtained a higher fertility factor (%). Similarly, the highest value for panicle length was observed for genotype Faker-e-Malakand, 1000-grains weight in genotype Calmochi, and maximum days to maturity was noticed in genotype Swati-2014. Moreover, the genotype Brio attained the highest value of stem diameter, while maximum seed length was noted in the genotype Sug Dasi. The highest number of primary branches plant^-1 in genotype Ibge-I and secondary branches plant^-1 in genotype Calmochi were noticed. A higher concentration of sodium and potassium was observed for the genotype Marte, while the genotype Muskan attained the maximum content of copper. Moreover, the highest concentration of iron in genotype Originario, zinc in genotype JP-5, and cadmium content were noticed in genotype Ibge. Similarly, the dendrogram analysis for quantitative parameters showed three clusters at 74.13% similarities. Whereas all the genotypes of European origin formed a separate cluster. A set of 5 simple sequence repeat primers, covering four chromosomes, amplified a total of 14 alleles and showed 100% polymorphism with an average PIC value ranging from 0.39 to 0.91. The UPGMA cluster analysis separated the 15 rice genotypes into 3 main groups based on 32.5% similarities and the highest genetic distance (45.1%) was observed between two genotypes (Fakher-e-malakand and Musa), having different geographical origins. There was no genetic distance between the genotypes Marte and Brio, irrespective of having the same origin.

CONCLUSIONS

The maximum genetic distances were noted for genotype, Fakhre-e-Malakand and Musa having a different origin, while the minimum genetic distance was shown by genotypes, Marte and Onice, from the same origin.

High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz)

Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower's genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.

Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/ . We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.

An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis)

Kompetitive allele-specific PCR (KASP) is a cost-effective single-step SNP genotyping technology, With an objective to enhance the marker repertoire and develop high efficient KASP-SNP markers in Chinese cabbage, we re-sequenced four Chinese cabbage doubled haploid (DH) lines, Y177-47, Y635-10, Y510-1 and Y510-9, and generated a total of more than 38.5 billion clean base pairs. A total of 827,720 SNP loci were identified with an estimated density of 3,217 SNPs/Mb. Further, a total of 387,354 SNPs with at least 30 bp to the next most adjacent SNPs on either side were selected as resource for KASP markers. From this resource, 258 (96.27%) of 268 SNP loci were successfully transformed into KASP-SNP markers using a Roche LightCycler 480-II instrument. Among these markers, 221 (85.66%) were co-dominant markers, 220 (85.27%) were non-synonymous SNPs, and 257 (99.6%) were newly developed markers. In addition, 53 markers were applied for genotyping of 34 Brassica rapa accessions. Cluster analysis separated these 34 accessions into three clusters based on heading types. The millions of SNP loci, a large set of resource for KASP markers, as well as the newly developed KASP markers in this study may facilitate further genetic and molecular breeding studies in Brassica rapa.

Fine mapping and candidate gene analysis of a seed glucosinolate content QTL, qGSL-C2, in rapeseed (Brassica napus L.)

QTL mapping and candidate gene analysis indicate that allelic variations in BnaC2.MYB28 resulted from homeologous exchange and determine difference in seed glucosinolate content. A low seed glucosinolate content has long been an important breeding objective in rapeseed improvement. However, the molecular mechanisms underlying seed GSL content variations remain to be elucidated in allotetraploid Brassica napus. Here, we developed a double haploid population from a cross between two B. napus accessions that possess relatively low, but significantly different seed GSL contents and identified a major QTL, qGSL-C2, on chromosome C02 that explains 30.88-72.87% of the phenotypic variation observed in five environments. Using near-isogenic lines, we further delimited qGSL-C2 to a physical region of 49 kb on the B. rapa chromosome A02 which is highly homologous to the target C02 interval. Among five candidate genes, BnaC2.MYB28, a homologue of the Arabidopsis MYB28 encoding a putative R2R3-MYB-type transcription factor functioning in aliphatic methionine-derived GSL synthesis, was most likely to be the target gene underlying the QTL. Sequence analysis revealed multiple insertion/deletion and SNP variations in the genomic region between the alleles of the NILs. Furthermore, the allelic variations in BnaC2.MYB28 in the natural B. napus population were significantly associated with seed GSL content. Remarkably, the phylogenetic analysis and sequence comparison suggested that while the BnaC2.MYB28 allele from the parental line G120 was inherited from B. oleracea BolC2.MYB28, its counterpart from the other parent, 9172, most likely evolved from B. rapa BraA2.MYB28 via possible homeologous exchange. Our study promotes greater understanding of the molecular regulation of seed GSL content and provides useful molecular markers for seed GSL improvement in B. napus.

ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea

BACKGROUND

Narrow genetic base, complex allo-tetraploid genome and presence of repetitive elements have led the discovery of single nucleotide polymorphisms (SNPs) in Brassica juncea (AABB; 2n = 4x = 36) at a slower pace. Double digest RAD (ddRAD) - a genome complexity reduction technique followed by NGS was used to generate a total of 23 million paired-end reads from three genotypes each of Indian (Pusa Tarak, RSPR-01 and Urvashi) and Exotic (Donskaja IV, Zem 1 and EC287711) genepools.

RESULTS

Sequence data analysis led to the identification of 10,399 SNPs in six genotypes at a read depth of 10x coverage among the genotypes of two genepools. A total of 44 hyper-variable regions (nucleotide variation hotspots) were also found in the genome, of which 93% were found to be a part of coding genes/regions. The functionality of the identified SNPs was estimated by genotyping a subset of SNPs on MassARRAY® platform among a diverse set of B. juncea genotypes. SNP genotyping-based genetic diversity and population studies placed the genotypes into two distinct clusters based mostly on the place of origin. The genotypes were also characterized for six morphological traits, analysis of which revealed a significant difference in the mean values between Indian and Exotic genepools for six traits. The association analysis for six traits identified a total of 45 significant marker-trait associations on 11 chromosomes of A- and B- group of progenitor genomes.

CONCLUSIONS

Despite narrow diversity, the ddRAD sequencing was able to identify large number of nucleotide polymorphisms between the two genepools. Association analysis led to the identification of common SNPs/genomic regions associated between flowering and maturity traits, thereby underscoring the possible role of common chromosomal regions-harboring genes controlling flowering and maturity in Brassica juncea.

New EST-SSR Markers for Individual Genotyping of Opium Poppy Cultivars (Papaver somniferum L.)

High-quality simple sequence repeat (SSR) markers are invaluable tools for revealing genetic variability which could be utilized for many purposes, such as breeding new varieties or the identifying current ones, among other applications. Based on the analysis of 3.7 million EST sequences and 15 genomic sequences from bacterial artificial chromosome (BAC) libraries, 200 trinucleotide genic (EST)-SSR and three genomic (gSSR) markers were tested, where 17 of them fulfilled all criteria for quality markers. Moreover, the reproducibility of these new markers was verified by two genetics laboratories, with a mean error rate per allele and per locus equal to 0.17%. These markers were tested on 38 accessions of Papaver somniferum and nine accessions of another five species of the Papaver and Argemone genera. In total, 118 alleles were detected for all accessions (median = 7; three to ten alleles per locus) and 88 alleles (median = 5; three to nine alleles per locus) within P. somniferum alone. Multivariate methods and identity analysis revealed high resolution capabilities of the new markers, where all but three pair accessions (41 out of 47) had a unique profile and opium poppy was distinguished from other species.

Development of molecular markers for invasive alien plants in Korea: a case study of a toxic weed, Cenchrus longispinus L., based on next generation sequencing data

BACKGROUND

Genomic data play an important role in plant research because of its implications in studying genomic evolution, phylogeny, and developing molecular markers. Although the information of invasive alien plants was collected, the genomic data of those species have not been intensively studied.

METHODS

We employ the next generation sequencing and PCR methods to explore the genomic data as well as to develop and test the molecular markers.

RESULTS

In this study, we characterize the chloroplast genomes (cpDNA) of Cenchrus longispinus and C. echinatus, of which the lengths are 137,144 and 137,131 bp, respectively. These two newly sequenced genomes include 78 protein-coding genes, 30 tRNA, and four rRNA. There are 56 simple single repeats and 17 forward repeats in the chloroplast genome of C. longispinus. Most of the repeats locate in non-coding regions. However, repeats can be found in infA, ndhD, ndhH, ndhK, psbC, rpl22, rpoC2, rps14, trnA-UGC, trnC-GCA, trnF-GAA, trnQ-UUG, trnS-UGA, trnS-GCU, and ycf15. The phylogenomic analysis revealed the monophyly of Cenchrus but not Panicum species in tribe Paniceae. The single nucleotide polymorphism sites in atpB, matK, and ndhD were successfully used for developing molecular markers to distinguish C. longispinus and related taxa. The simple PCR protocol for using the newly developed molecular markers was also provided.

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP "hotspots," and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when r² = 0.1, but the LD decay in the A genome (43 kb) was much shorter than in the C genome (1,455 kb), supporting the targeted introgression of the A genome from progenitor species B. rapa into Chinese rapeseed. This study also lays the foundation for genetic analysis of important agronomic traits using this rapeseed population.

Ultraestrutura celular e expressão de proteínas de leveduras hanseniaspora sob efeito do estresse etanólico

Resumo O objetivo deste estudo foi avaliar a resposta de Hanseniaspora opuntiae (Ho41) e H. guilliermondii (Hg43) ao estresse etanólico, observando a ultraestrutura e o perfil de expressão proteica em concentrações crescentes de etanol. A ultraestrutura foi analisada por microscopia eletrônica de varredura (MEV) e a expressão proteica, pelo perfil eletroforético (SDS-PAGE). Na análise microscópica, as cepas em meio Yeast Malt Agar sem etanol mostraram células jovens com morfologia apiculada, brotamento bilateral e polos distais côncavos. Com o início do estresse, a 3% de etanol, as células apresentaram múltiplas cicatrizes em forma de anéis e, com 6%, alterações na integridade da parede celular, plasmólise e ativação da autólise. Na análise eletroforética, observou-se, tanto para Ho41 quanto para Hg43, aumento na expressão de um peptídeo de 100 kDa, com aumento do etanol no meio, indicando ser uma proteína de choque térmico (HSP). As HSPs vêm sendo patenteadas como marcadores de organismos de interesse biotecnológico, já que as condições necessárias para obtenção de bioprodutos muitas vezes requerem cultivo sob estresse. Neste contexto, esta proteína pode ser indicada como marcador molecular para bioprospecção ou melhoramento genético de cepas não-saccharomyces mais resistentes aos processos de fermentação, na fabricação de vinhos.

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP "hotspots," and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when r² = 0.1, but the LD decay in the A genome (43 kb) was much shorter than in the C genome (1,455 kb), supporting the targeted introgression of the A genome from progenitor species B. rapa into Chinese rapeseed. This study also lays the foundation for genetic analysis of important agronomic traits using this rapeseed population.

Microsatellite markers: what they mean and why they are so useful

Microsatellites or Single Sequence Repeats (SSRs) are extensively employed in plant genetics studies, using both low and high throughput genotyping approaches. Motivated by the importance of these sequences over the last decades this review aims to address some theoretical aspects of SSRs, including definition, characterization and biological function. The methodologies for the development of SSR loci, genotyping and their applications as molecular markers are also reviewed. Finally, two data surveys are presented. The first was conducted using the main database of Web of Science, prospecting for articles published over the period from 2010 to 2015, resulting in approximately 930 records. The second survey was focused on papers that aimed at SSR marker development, published in the American Journal of Botany's Primer Notes and Protocols in Plant Sciences (over 2013 up to 2015), resulting in a total of 87 publications. This scenario confirms the current relevance of SSRs and indicates their continuous utilization in plant science.

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16-74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7-8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice.