Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops

Evaluation and characteristic analysis of SSRs from the transcriptomic sequences of Perilla crop (Perilla frutescens L.)

Perilla crop is a self-fertilizing annual plant, cultivated and used mainly in East Asia. Perilla frutescens var. frutescens seeds are rich in unsaturated fatty acids, which have health benefits, and Perilla frutescens var. crispa leaves are rich in anthocyanins. However, genomic analysis such as whole genome sequencing or genetic mapping has not been performed on Perilla crop. This current study confirms the abundance and diversity of 15,991 simple sequence repeats (SSRs) classified in previous studies in the Perilla genome, selects and designs 1,538 SSR primer sets, and confirms which SSR primer sets exhibit high polymorphism. Of the 15,991 SSRs classified, there were 9,910 (62%) dinucleotide repeats, 5,652 (35.3%) trinucleotide repeats, and 429 (2.7%) tetranucleotide repeats. Among these, the most identified was (CT)n with a total of 4,817. The 15,991 SSRs had 4 to 26 repeats. Four repeats were the most frequent with 11,084 (69.3%). A total of 1,538 SSR primers were selected and designed to confirm polymorphism, of which 157 showed persistent and clear polymorphism. Among these 157 SSR primer sets, 98 (62.4%) were dinucleotide repeats, 39 (24.8%) were trinucleotide repeats, and 20 (12.7%) were tetranucleotide repeats. Among 549 SSR primers that showed polymorphism, trinucleotide repeats showed persistent polymorphism at a high rate. Therefore, when developing SSR primer sets for Perilla crop in the future, it is recommended that trinucleotide repeats be selected first. These research results will be helpful in future genomic analysis and development of SSR primers in Perilla crop.

Development of microsatellite markers and evaluation of the genetic diversity of the edible sea anemone Paracondylactissinensis (Cnidaria, Anthozoa) in China

Paracondylactissinensis Carlgren, 1934 is a sea anemone with economic value in China. The wild population of P.sinensis has been shrinking due to overfishing and environmental pollution, which have caused price instability. In winter, the price of P.sinensis can reach 25 USD per kilogram. Up to now, there are no genetic markers developed for P.sinensis, preventing a further exploration of their population genetic diversity. In this study, the full-length transcriptome of P.sinensis was sequenced and microsatellite DNA markers (simple sequence repeats [SSRs]) were developed from those transcripts. A total of 52 primer pairs, which can amplify specific polymorphic bands in PCR experiments, were designed for the SSR markers. Genetic diversity and population genetics were analysed for P.sinensis populations collected from the coasts of Taizhou and Rizhao using six microsatellite DNA loci. While inbreeding was detected in both populations (Fis > 0), the overall number of alleles (Na = 11.3) and bottleneck analysis suggested that the genetic diversity of P.sinensis has not been greatly impacted. Clustering analyses using STRUCTURE, principal coordinate analysis and unweighted pair group method with arithmetic mean tree revealed that the Taizhou population diverged from the Rizhao population; however, the genetic differentiation between the populations was moderate. Human-mediated commercial activities may be the principal reasons for the gene flow between the populations. Our study provides the first evaluation of the genetic resources of wild P.sinensis populations in China, which can serve as a useful reference for future comparative studies on population genetics and may guide policy-makers in initiating strategies for germplasm conservation and artificial breeding.

Assessment of Population Genetic Diversity of Medicinal Meconopsis integrifolia (Maxim.) Franch. Using Newly Developed SSR Markers

Meconopsis integrifolia is an endangered Tibetan medicinal plant with significant medicinal and ornamental value. Understanding its genetic diversity and structure is crucial for its sustainable utilization and effective conservation. Here, we develop a set of SSR markers based on transcriptome data to analyze the genetic diversity and structure of 185 individuals from 16 populations of M. integrifolia. The results indicate that M. integrifolia exhibits relatively high genetic diversity at the species level (the percentage of polymorphic bands PPB = 91.67%, Nei's genetic diversity index He = 0.2989, Shannon's information index I = 0.4514) but limited genetic variation within populations (PPB = 12.08%, He = 0.0399, I = 0.0610). The genetic differentiation among populations is relatively high (the coefficient of gene differentiation GST = 0.6902), and AMOVA analysis indicates that 63.39% of the total variation occurs among populations. This suggests that maintaining a limited number of populations is insufficient to preserve the overall diversity of M. integrifolia. Different populations are categorized into four representative subclusters, but they do not cluster strictly according to geographical distribution. Limited gene flow (Nm = 0.2244) is likely the main reason for the high differentiation among these populations. Limited seed and pollen dispersal abilities, along with habitat fragmentation, may explain the restricted gene flow among populations, highlighting the necessity of conserving as many populations in the wild as possible.

Banana Classification Using Sanger Sequencing of the Ribosomal DNA Internal Transcribed Spacer (ITS) Region

Banana (Musa spp.) is one of the most economically important horticultural crops. There are many types of banana, with differing ploidy (usually diploid, triploid, or tetraploid) and genome types (most containing the A or/and B genome). Currently, observation and genome type detection are commonly used to identify banana germplasm resources. However, observation is tedious, while genome type detection cannot distinguish categories below genome types. It is, therefore, urgent to establish a simple and effective method for identifying banana germplasm resources. This study sequenced and analyzed the ribosomal DNA internal transcribed spacer (ITS) sequences of 62 banana germplasm resources and found that the sequencing peaks, especially the 20 bp region near the 420-bp position (referred to as the 420-bp region), exhibited relatively recognizable and repeatable polymorphism characteristics. Using the 420-bp region as a marker, we were able to quickly distinguish bananas belonging to different genome type groups or different subgroups in the same genome type group. Moreover, it appeared that Sanger sequencing of ITS could be used to identify hybrid banana offspring. In general, ITS sequencing simplifies the classification of banana germplasm resources and has potential application in several areas of Musa improvement.

Association Mapping of Seed Coat Color Characteristics for Near-Isogenic Lines of Colored Waxy Maize Using Simple Sequence Repeat Markers

Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method for identifying genetic markers associated with complex traits. Our study aimed to identify molecular markers associated with two anthocyanin content and six seed coat color traits in near-isogenic lines (NILs) of colored waxy maize assessed through AMA. We performed AMA for 285 SSR loci and two anthocyanin content and six seed coat color traits in 10 NILs of colored waxy maize. In the analysis of population structure and cluster formation, the two parental lines (HW3, HW9) of "Mibaek 2ho" variety waxy maize and the 10 NILs were clearly divided into two groups, with each group containing one of the two parental inbred lines. In the AMA, 62 SSR markers were associated with two seed anthocyanin content and six seed coat color traits in the 10 NILs. All the anthocyanin content and seed coat color traits were associated with SSR markers, ranging from 2 to 12 SSR markers per characteristic. The 12 SSR markers were together associated with both of the two anthocyanin content (kuromanin and peonidin) traits. Our current results demonstrate the effectiveness of SSR analysis for the examination of genetic diversity, relationships, and population structure and AMA in 10 NILs of colored waxy maize and the two parental lines of the "Mibaek 2ho" variety waxy maize.

Determination of genomic regions associated with early storage root formation and bulking in cassava

Early cassava storage root formation and bulking is a medium of escape that farmers and processors tend to adopt in cases of abiotic and biotic stresses like drought, flood, and destruction by domestic animals. In this study, 220 cassava genotypes from the International Institute of Tropical Agriculture (IITA), National Root Crops Research Institute (NRCRI), International Center for Tropical Agriculture (CIAT), local farmers (from farmer's field), and NextGen project were evaluated in three locations (Umudike, Benue, and Ikenne). The trials were laid out using a split plot in a randomized incomplete block design (alpha lattice) with two replications in 2 years. The storage roots for each plant genotype were sampled or harvested at 3, 6, 9, and 12 month after planting (MAP). All data collected were analyzed using the R-statistical package. The result showed moderate to high heritability among the traits, and there were significant differences (p< 0.05) among the performances of the genotypes. The genome-wide association mapping using the BLINK model detected 45 single-nucleotide polymorphism (SNP) markers significantly associated with the four early storage root bulking and formation traits on Chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 10, 13, 14, 17, and 18. A total of 199 putative candidate genes were found to be directly linked to early storage root bulking and formation. The functions of these candidate genes were further characterized to regulate i) phytohormone biosynthesis, ii) cellular growth and development, and iii) biosynthesis of secondary metabolites for accumulation of starch and defense. Genome-wide association study (GWAS) also revealed the presence of four pleiotropic SNPs, which control starch content, dry matter content, dry yield, and bulking and formation index. The information on the GWAS could be used to develop improved cassava cultivars by breeders. Five genotypes (W940006, NR090146, TMS982123, TMS13F1060P0014, and NR010161) were selected as the best early storage root bulking and formation genotypes across the plant age. These selected cultivars should be used as sources of early storage root bulking and formation in future breeding programs.

Association mapping analysis for cultivated and weedy types of Perilla crop collected from South Korea using morphological characteristics and SSR markers

There are two cultivated and weedy types of Perilla crop (TCWTPC), and they are widely distributed and cultivated in East Asia, especially in South Korea and Japan. The objective of this study is to create simple sequence repeat (SSR) markers linked to morphological traits that show differences between accessions of the TCWTPC using recently designed SSR primer sets in Perilla crop. Genetic diversity within 52 accessions of the TCWTPC, gathered from South Korea, was assessed using 28 novel Perilla SSR primer sets. Based on the assessment, a collection of 28 Perilla SSR primer sets were shown to exhibit polymorphism and yielded a total of 142 alleles across the 52 accessions of the TCWTPC. Through inspection of a phylogenetic tree and population structure, the 52 accessions of the TCWTPC were classified into three major groups. Although most accessions of the TCWTPC were relatively clearly distinguished, SSR markers failed to distinguish several accessions belonging to the two weedy types of the Perilla crop. By using an association mapping analysis (AMA) of the 28 Perilla SSR markers and seven morphological characteristics in the 52 TCWTPC accessions, we detected that three of the Perilla SSR markers (KNUPF134, KNUPF137, KNUPF149) were associated with plant and seed characteristics. The novel SSR primer sets developed in Perilla crop should be useful in AMA for assessing genetic diversity and relationships between and within TCWTPC accessions, and this information will be helpful for genetic mapping in breeding programs for Perilla crop.

Association Mapping for Evaluation of Population Structure, Genetic Diversity, and Physiochemical Traits in Drought-Stressed Maize Germplasm Using SSR Markers

Globally, maize is one of the most consumed crops along with rice and wheat. However, maize is sensitive to different abiotic stress factors, such as drought, which have a significant impact on its production. The aims of this study were to investigate (1) genetic variation among 41 maize-inbred lines and the relationships among them and (2) significant marker-trait associations (SMTAs) between 7 selected physiochemical traits and 200 simple sequence repeat (SSR) markers to examine the genetics of these traits. A total of 1023 alleles were identified among the 41 maize-inbred lines using the 200 SSR loci, with a mean of 5.1 alleles per locus. The average major allele frequency, gene diversity, and polymorphism information content were 0.498, 0.627, and 0.579, respectively. The population structure analysis based on the 200 SSR loci divided the maize germplasm into two primary groups with an admixed group. Moreover, this study identified, respectively, 85 SMTAs and 31 SMTAs using a general linear model (Q GLM) and a mixed linear model (Q  + K MLM) with statistically significant (p < 0.05 and <0.01) associations with the seven physiochemical traits (caffeic acid content, chlorogenic acid content, gallic acid content, ferulic acid content, 2,2-diphenyl-1-picrylhydrazyl free radical scavenging activity, leaf relative moisture content, total phenolic content). These SSR markers were highly correlated with one or more of the seven physiochemical traits. This study provides insights into the genetics of the 41 maize-inbred lines and their seven physiochemical traits and will be of assistance to breeders in the marker-assisted selection of maize for breeding programs.

Genetic diversity analysis and fingerprint construction of Korean pine (Pinus koraiensis) clonal seed orchard

Korean pine is a native tree species in Northeast China. In order to meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of Korean pine, we collected Korean pine clones from 7 populations in Northeast China, analyzed the genetic diversity and genetic structure by SSR molecular marker technology and clustered them to revealed the inter- and intrapopulation differentiation characteristics of each clone. The fingerprint profiles of 161 Korean pine clones were also constructed. 77 alleles were detected for 11 markers, and 18 genotypes were identified on average for each marker. The PIC of the different markers ranged from 0.155-0.855, and the combination of PI and PIsibs for the 11 markers was 3.1 × 10-8 and 1.14 × 10-3, respectively. MANOVA showed that genetic variation existed mainly within populations, accounting for 98% of the total variation. The level of genetic differentiation among populations was low, with an average Nm between populations of 11.036. Genetic diversity is lower in the Lushuihe population and higher in the Tieli population. The 161 Korean pine clones were divided into 4 or 7 populations, and the 7 populations were not clearly distinguished from each other, with only the Lushuihe population showing partial differentiation. There is no significant correlation between the genetic distance of Korean pine populations and the geographical distance of their superior tree sources. This result can provide recommendations for future Korean pine breeding programs. The combination of 11 markers could completely distinguish 161 clones and establish the fingerprint. Genetic diversity of Korean pine clones from the 7 populations was abundant, and the genetic distances of individuals and populations were evenly dispersed. The fingerprint map can be used for the identification of Korean pine clones.

Utilization of Novel Perilla SSR Markers to Assess the Genetic Diversity of Native Perilla Germplasm Accessions Collected from South Korea

The Perilla crop is highly regarded in South Korea, both as a health food and traditional food. However, there is still a lack of Perilla SSR primer sets (PSPSs) for studying genetic variation among accessions of cultivated and weedy types of Perilla crop (CWTPC) from South Korea. In this study, 30 PSPSs were newly developed based on transcriptome contigs in P. frutescens, and 17 of these PSPSs were used to study the genetic diversity, phylogenetic relationships and structure population among 90 accessions of the CWTPC collected from South Korea. A total of 100 alleles were detected from selected 17 PSPSs, with an average of 5.9 alleles per locus. The gene diversity (GD) ranged from 0.164 to 0.831, with an average of 0.549. The average GD values from the cultivated var. frutescens, weedy var. frutescens, and weedy var. crispa, were 0.331, 0.588, and 0.389 respectively. In addition, most variance shown by Perilla SSR markers was within a population (73%). An analysis of the population structure and phylogenetic relationships showed that the genetic relationship among accessions of the weedy var. frutescens and weedy var. crispa is closer than that for the accessions of the cultivated var. frutescens. Based on association analysis between 17 PSPSs and three seed traits in 90 Perilla accessions, we detected 11 PSPSs that together were associated with the seed size and seed hardness traits. Therefore, the newly developed PSPSs will be useful for analyzing genetic variation among accessions of the CWTPC, association mapping, and selection of important morphological traits in Perilla crop breeding programs.

Genetic Diversity and Population Structure of Normal Maize Germplasm Collected in South Sudan Revealed by SSR Markers

Maize is one of the leading global cereals, and in South Sudan maize cultivation occurs in nearly all of the country's agro-ecological zones. Despite its widespread cultivation, farmers in South Sudan depend on undeveloped varieties, which results in very low yields in the field. In the current study, 27 simple sequence repeat (SSR) markers were used to investigate genetic diversity and population structures among 37 landrace maize accessions collected from farmers' fields in South Sudan. In total, 200 alleles were revealed with an average of 7.4 alleles per locus and a range from 3.0 to 13.0 alleles per locus. The observed heterozygosity values ranged from 0.06 to 0.91 with an average of 0.35. High polymorphic information content (PIC) values were identified with a mean of 0.69, which indicates the informativeness of the chosen SSR loci. Genetic structure analysis revealed a moderate genetic differentiation among the maize populations with a fixation index of 0.16, while there was very high genetic differentiation within the groups of populations of three regions with a mean fixation index (F) of 0.37. An unweighted pair group method with an arithmetic mean (UPGMA) dendrogram clustered the 37 maize accessions into three groups with 43% genetic similarity. The clustering pattern of the maize accessions was moderately consistent with their collection area. The findings of this study will provide maize breeders with a better understanding of maize diversification as well as a reserve of genetic resources for use in the selection of advantageous and useful resources for the development of maize varieties in South Sudan.

Genetic variation of seed oil characteristics in native Korean germplasm of Perilla crop (Perilla frutescens L.) using SSR markers

BACKGROUND

In order to maximize the use of valuable native Perilla germplasm in South Korea, knowledge of the Perilla seed oil content and genetic variation among native Perilla germplasm resources is very important for the conservation and development of new Perilla seed oil varieties using the native Perilla germplasm accessions preserved from the Rural Development Administration Genebank (RDA-Genebank) collection from South Korea.

OBJECTIVES

In this study, we studied population structure and association mapping to identify Perilla SSR markers (PSMs) associated with the five fatty acid contents and two seed characteristics of the native Korean Perilla germplasm accessions of cultivated var. frutescens of the RDA-Genebank collected in South Korea.

METHODS

For an association mapping analysis to find PSMs associated with the five fatty acid contents and two seed characteristics of the Perilla germplasm accessions of cultivated var. frutescens, we evaluated the content of five fatty acids of 280 native Korean Perilla germplasm accessions and used 29 Perilla SSR primer sets to measure the genetic diversity and relationships, population structure, and association mapping of the native Korean Perilla germplasm accessions of the RDA-Genebank collected in South Korea.

RESULTS

Five fatty acids of 280 native Korean Perilla accessions were identified as follows: palmitic acid (PA) (5.30-8.66%), stearic acid (SA) (1.60-4.19%), oleic acid (OA) (9.60-22.5%), linoleic acid (LA) (8.38-25.4%), and linolenic acid (LNA) (52.7-76.4%). In a correlation analysis among the five fatty acids and two seed characteristics of the 280 Perilla accessions, the combinations of PA and SA (0.794**) and SA and OA (0.724**) showed a particularly high positive correlation coefficients compare to other combinations. By using an association analysis of the 29 PSMs and the five fatty acids in the 280 Perilla accessions, we found 17 PSMs (KNUPF1, KNUPF2, KNUPF4, KNUPF10, KNUPF16, KNUPF25, KNUPF26, KNUPF28, KNUPF37, KNUPF55, KNUPF62, KNUPF71, KNUPF74, KNUPF77, KNUPF85, KNUPF89, and KNUPF118) associated with the content of the five fatty acid components and two seed characteristics.

CONCLUSIONS

These PSMs are considered to be useful molecular markers related to five fatty acid components and two seed characteristics for selecting accessions from the germplasm accessions of the Perilla crop and their related weedy types through association mapping analysis and marker-assisted selection (MAS) breeding programs.

Construction of a core collection of native Perilla germplasm collected from South Korea based on SSR markers and morphological characteristics

The leaves and seed oil of Perilla crop (Perilla frutescens L.) have attracted interest as health foods in East Asia. This crop has been traditionally cultivated and used for a long time as a folk plant, especially in Korea. In our study, the 22 SSR markers and eight morphological traits were used to assess the genetic diversity and population structure, to select a core collection of 400 Perilla accessions conserved in the RDA-Genebank of South Korea. A total of 173 alleles were detected and the number of alleles per locus ranged from 4 to 15 (average = 7.9). Gene diversity and polymorphic information content ranged from 0.138 to 0.868 (average = 0.567) and 0.134 to 0.853 (average = 0.522), respectively. The 400 accessions were not clearly distinguished geographically by STRUCTURE and UPGMA analyses. A core collection (44 accessions) was selected from the entire collection by using PowerCore. The core collection accounted for 11.0% of the entire Perilla collection, including 100% of the number of alleles maintained in the whole collection and with similar or greater Shannon-Weaver and Nei diversity indices than the whole collection. The core collection selected by SSR markers was evenly distributed in three clusters on a scatter plot by eight morphological traits. The first core collection of Perilla accessions was constructed, and it maintained allelic richness. Further modification of the core collection is expected with the continuous addition of new accessions of the two cultivated types of Perilla crop and their weedy types.

Genetic variability and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm

Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei’s genetic distance, heterozygosity, Shannon’s information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei’s genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea.

Genetic Variation of Native Perilla Germplasms Collected from South Korea Using Simple Sequence Repeat (SSR) Markers and Morphological Characteristics

Using morphological characteristics and simple sequence repeat (SSR) markers, we evaluated the morphological variation and genetic diversity of 200 Perilla accessions collected from the five regions of South Korea and another region. In morphological characteristics analysis, particularly leaf color, stem color, degree of pubescence, and leaf size have been found to help distinguish the morphological features of native Perilla accessions cultivated in South Korea. Twenty SSR primer sets confirmed a total of 137 alleles in the 200 Perilla accessions. The number of alleles per locus ranged from 3 to 13, with an average number of alleles per locus of 6.85. The average genetic diversity (GD) was 0.649, with a range of 0.290–0.828. From analysis of SSR markers, accessions from the Jeolla-do and Gyeongsang-do regions showed comparatively high genetic diversity values compared with those from other regions in South Korea. In the unweighted pair group method with arithmetic mean (UPGMA) analysis, the 200 Perilla accessions were found to cluster into three main groups and an outgroup with 42% genetic similarity, and did not show a clear geographic structure from the five regions of South Korea. Therefore, it is believed that landrace Perilla seeds are frequently exchanged by farmers through various routes between the five regions of South Korea. The results of this study are expected to provide interesting information on the conservation of these genetic resources and selection of useful resources for the development of varieties for seeds and leafy vegetables of cultivated Perilla frutescens var. frutescens in South Korea.

Identifying SSR Markers Related to Seed Fatty Acid Content in Perilla Crop (Perilla frutescens L.)

Perilla seed oil has been attracting attention in South Korea as a health food. Five fatty acids of 100 Perilla accessions were identified as follows: palmitic acid (PA) (5.10-9.13%), stearic acid (SA) (1.70-3.99%), oleic acid (OA) (11.1-21.9%), linoleic acid (LA) (10.2-23.4%), and linolenic acid (LNA) (54.3-75.4%). Additionally, the 100 Perilla accessions were divided into two groups (high or low) based on the total fatty acid content (TFAC). By using an association analysis of 40 simple sequence repeat (SSR) markers and the six Perilla seed oil traits in the 100 Perilla accessions, we detected four SSR markers associated with TFAC, five SSR markers associated with LNA, one SSR marker associated with LA, two SSR markers each associated with OA and PA, and four SSR markers associated with SA. Among these SSR markers, four SSR markers (KNUPF14, KNUPF62, KNUPF72, KNUPF85) were all associated with TFAC and LNA. Moreover, two SSR markers (KNUPF62, KNUPF85) were both associated with TFAC, LNA, and OA. Therefore, these SSR markers are considered to be useful molecular markers for selecting useful accessions related to fatty acid contents in Perilla germplasm and for improving the seed oil quality of Perilla crop through marker-assisted selection (MAS) breeding programs.

Revisiting traditional SSR based methodologies available for elephant genetic studies

Asian elephant (Elephas maximus) plays a significant role in natural ecosystems and it is considered as an endangered animal. Molecular genetics studies on elephants' dates back to 1990s. Microsatellite markers have been the preferred choice and have played a major role in ecological, evolutionary and conservation research on elephants over the past 20 years. However, technical constraints especially related to the specificity of traditionally developed microsatellite markers have brought to question their application, specifically when degraded samples are utilized for analysis. Therefore, we analyzed the specificity of 24 sets of microsatellite markers frequently used for elephant molecular work. Comparative wet lab analysis was done with blood and dung DNA in parallel with in silico work. Our data suggest cross-amplification of unspecific products when field-collected dung samples are utilized in assays. The necessity of Asian elephant specific set of microsatellites and or better molecular techniques are highlighted.

Genetic characterization and association mapping in near-isogenic lines of waxy maize using seed characteristics and SSR markers

BACKGROUND

Association mapping has been advocated as the method of choice for identifying loci involved in the inheritance of complex traits in crop species. This method involves identifying markers with significant differences in allele frequency between individuals with a phenotype of interest and a set of unrelated control individuals.

OBJECTIVE

The purpose of our study is not only to investigate the genetic diversity and relationships of the basic molecular markers of near-isogenic lines (NILs) of waxy maize, but it is also to identify molecular markers related to interesting seed characteristics including 4 seed quantity traits and 4 seed phenotypic traits using association analysis with population structure.

METHODS

We performed association mapping of 200 SSR markers and 8 seed characteristics among 10 NILs of waxy maize and two parental lines (HW3, HW9) (recurrent parent) of "Mibaek 2" variety.

RESULTS

In population structure and cluster analysis, the 10 NILs and two parental lines were divided into two groups. Seven inbred lines, including HW3, were assigned to Group I. Group II contained 5 inbred lines, including HW9. In addition, we found that 32 SSR markers associate with 8 seed characteristics in 10 NILs. In particular, five SSR markers (umc1986, umc1747, umc2275, phi078, umc1366) were together associated with more than one seed characteristics such as EL, 100 KW, SCC, R, L*, and V.

CONCLUSION

This study demonstrated the utility of SSR analysis for studying GD, population structure, and association mapping in 10 NILs and two parental lines (HW3, HW9) of "Mibaek 2" variety.

Identifying SSR markers associated with seed characteristics in Perilla (Perilla frutescens L.)

Substantial differences exist in seed dormancy between cultivated crops and their wild progenitors. The purpose of this study was to identify simple sequence repeat (SSR) markers associated with seed characteristics in cultivated and weedy types of Perilla crop. By using an association analysis of 29 SSR markers and three seed traits in 38 Perilla accessions, we detected six SSR markers associated with the seed germination rate (SGR), eight SSR markers associated with seed hardness (SH), and seven SSR markers associated with seed size (SS). Among these SSR markers, three (KNUPF3, KNUPF25, KNUPF60) were associated with the SGR, SH, and SS traits. Correlation analysis among the three seed traits of the 38 Perilla accessions showed a positive correlation coefficient for the combination of SGR and SS (0.811**) and a negative correlation coefficient for the combinations of SGR and SH (- 0.706**), and SS and SH (- 0.899**). A phylogenetic tree constructed using the unweighted pair group method with arithmetic mean (UPGMA) revealed that accessions of cultivated P. frutescens var. frutescens could be distinguished from weedy accessions of P. frutescens var. frutescens and P. frutescens var. crispa using the 29 SSR markers. Selected SSR markers related to the three seed traits distinguished accessions of cultivated and weedy types. Therefore, these results are very important for understanding the seed characteristics of cultivated and weedy types of Perilla crop. It will further help for improving the seed quality of Perilla crop through marker-assisted selection (MAS) breeding programs.

SUPPLEMENTARY INFORMATION

The online version of this article (10.1007/s12298-021-00933-3) contains supplementary material, which is available to authorized users.

Assessment of genetic diversity and population structure among a collection of Korean Perilla germplasms based on SSR markers

BACKGROUND

Information on the genetic variation of genetic resource collections is very important for both the conservation and utilization of crop germplasms in genebanks. Var. frutescens of Perilla crop is extensively cultivated in South Korea as both an oil crop and a vegetable crop.

OBJECTIVES

We used SSR markers to evaluate the genetic diversity, genetic relationships, and population structure of 155 accessions of var. frutescens that have been selected as genetic resources for the development of leaf vegetable cultivars and preserved in the RDA-Genebank collection from South Korea.

METHODS

A total of 155 accessions of var. frutescens of Perilla crop collected in South Korea were obtained from the RDA-Genebank of the Republic of Korea. We selected 20 SSR markers representing the polymorphism of and adequately amplifying all the Perilla accessions.

RESULTS

The average GD and PIC values were 0.642 and 0.592, respectively, with ranges of 0.244-0.935 and 0.232- 0.931. The genetic variability in the southern region of South Korea was higher than that in the central region. The clustering patterns were not clearly distinguished between the accessions of var. frutescens from the central and southern regions of South Korea.

CONCLUSION

These results regarding the genetic diversity and population structure of the 155 accessions of var. frutescens of South Korea provide useful information for understanding the genetic variability of this crop and selecting and managing core germplasm sets in the RDA-Genebank of the Republic of Korea.

First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Genus Salvadora

Salvadoraceae constitutes ecologically imperative desert families of 3 genera-Azima, Dobera and Salvadora. Under genus Salvadora of this family, S. oleoides is a keystone species of socio-economic and medicinal value. This species naturally grows in the arid zones but currently experiencing severe fragmentation due to land use change and reduced regeneration, which may have resulted in the depletion of genetic diversity. Hence, it is up-most important to develop genomic resources for studying the population genetics in S. oleoides. This study aims to develop robust microsatellites markers, which were not yet reported in genus Salvodora due to lack of genome sequence information. We developed novel microsatellites markers in S. oleoides using Illumina paired-end sequencing technology. In total, 14,552 simple sequence repeat (SSR) markers were successfully designed from 21,055 microsatellite repeats detected in the 13 Gb raw sequence data. Afterwards, a subset of 101 SSRs were randomly selected and validated, 94 primers were successfully amplified and 34 showed polymorphisms. These SSRs were used to estimate the measures of genetic diversity in three natural populations of state Rajasthan and Gujarat. Importantly, average number of alleles (N_a), observed heterozygosity (H_o), expected heterozygosity (H_e), and polymorphism information content (PIC) were recorded as 2.4, 0.529, 0.357, and 0.326, respectively. Furthermore, 15 primers were evaluated in S. persica for cross-transferability, and all were successfully amplified but only eight showed polymorphisms. This study has been conducted first time for S. oleoides and pioneer among the native species of arid-zone in India.

Genetic characterization of cassava (Manihot esculenta Crantz) genotypes using agro-morphological and single nucleotide polymorphism markers

Dearth of information on extent of genetic variability in cassava limits the genetic improvement of cassava genotypes in Sierra Leone. The aim of this study was to assess the genetic diversity and relationships within 102 cassava genotypes using agro-morphological and single nucleotide polymorphism markers. Morphological classification based on qualitative traits categorized the germplasm into five different groups, whereas the quantitative trait set had four groups. The SNP markers classified the germplasm into three main cluster groups. A total of seven principal components (PCs) in the qualitative and four PCs in the quantitative trait sets accounted for 79.03% and 72.30% of the total genetic variation, respectively. Significant and positive correlations were observed between average yield per plant and harvest index (r = 0.76***), number of storage roots per plant and harvest index (r = 0.33*), height at first branching and harvest index (0.26*), number of storage roots per plant and average yield per plant (r = 0.58*), height at first branching and average yield per plant (r = 0.24*), length of leaf lobe and petiole length (r = 0.38*), number of leaf lobe and petiole length (r = 0.31*), width of leaf lobe and length of leaf lobe (r = 0.36*), number of leaf lobe and length of leaf lobe (r = 0.43*), starch content and dry matter content (r = 0.99***), number of leaf lobe and root dry matter (r = 0.30*), number of leaf lobe and starch content (r = 0.28*), and height at first branching and plant height (r = 0.45**). Findings are useful for conservation, management, short term recommendation for release and genetic improvement of the crop.

Ecotypes or phenotypic plasticity-The aquatic and terrestrial forms of Helosciadium repens (Apiaceae)

Morphological and ecological differences of two forms of Helosciadium repens are known and described in the literature: aquatic and terrestrial. However, their taxonomic status is currently unknown. The question whether they are genotypically adapted to specific environmental conditions or are those differences a result of phenotypic plasticity is addressed in this study.SSR and ISSR data were used to uncover genotypic differences. Data from drought stress experiments (system water content and relative water content of leaves) were used to evaluate the response to water as an environmental factor. The stomatal index of both forms grown under different water treatments was analyzed.The principal component analysis of the ISSR data revealed no clustering that would correspond with ecotypes. The diversity parameters of the SSR data showed no significant differences. The aquatic populations showed a tendency toward heterozygosity, while the terrestrial ones showed a bias toward homozygosity. Both forms responded similarly to the changes in water availability, with newly produced leaves after drought stress that were better adapted to repeated drought stress. Stomatal indices were higher in plants from aquatic habitats, but these differences disappeared when the plants were grown in soil.The observed responses indicate that the differences between forms are due to phenotypic plasticity.

Genetic diversity and population structure analysis of Asian and African aromatic rice (Oryza sativa L.) genotypes

Rice germplasms collected from different regions could be used as valuable resources for the future breeding programme. For the utilization of such collections, knowledge about the level and distribution of genetic diversity among these collections will facilitate the breeder. In this study, we report the phenotypic correlation, biochemical quality parameters and population genetic analysis of 35 rice accessions including 34 aromatic rice from different countries and a nonaromatic, Nagina 22, a well-known drought resistance variety. Further biochemical quality analysis, gel consistency test, molecular diversity analysis with 55 simple sequence repeat markers, population structure analysis and pair wise F_ST analysis were also conducted to assess the genetic diversity. The collected rice genotypes showed significant variability in different agronomic traits, i.e. spikelet per panicle, branches per panicle etc. Results obtained from the above tests demonstrated the importance of regional genetic studies for understanding the diversification of aromatic rice in Asian and African rice.

Genetic diversity and population structure of Perilla frutescens collected from Korea and China based on simple sequence repeats (SSRs)

BACKGROUND

Perilla frutescens (L.) Britt. is divided into two varieties based on morphology and use. One is P. frutescens var. frutescens, which is used both as a leafy vegetable and as an oil obtained from the seeds. The other variety is P. frutescens var. crispa, a Chinese medicine or spice vegetable crop. In addition, weedy types of var. frutescens and var. crispa are occasionally grown as relict forms and are easy to find on roadsides, in waste areas and around farmers' fields or farmhouses. SSR markers have been successfully used to examine the genetic diversity and relationships of cultivated and weedy types of Perilla in many regions.

OBJECTIVES

In this study, we used 25 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 90 Perilla accessions from Korea and China.

METHODS

A total of 90 accessions of Perilla were collected in Korea and China included 45 accessions from each of Korea and China. We selected 25 SSR markers representing the polymorphism of and adequately amplifying all the Perilla accessions.

RESULTS

A total of 153 alleles were identified, with an average of 6.12 alleles per locus. The GD level and PIC value for cultivated and weedy types of P. frutescens from China were higher than those for accessions from Korea. Weedy accessions had higher GD and PIC values than cultivated accessions. In the population structure analysis using the model-based method, the 90 Perilla accessions were divided into two main group and an admixed group based on a membership probability threshold of 0.8. Based on the distance-based unweighted pair group method with the arithmetic mean (UPGMA), all accessions were classified into four major groups with a genetic similarity of 32.8%.

CONCLUSION

Finally, the findings of this study will provide useful theoretical knowledge for further study of the population structure and genetic diversity of Perilla species and benefit Perilla crop breeding and germplasm conservation in Korea and China.

Ecotype-Level Genetic Biodiversity of Five Italian Traditional Crops

Italy displays a high level of agrobiodiversity due to its diversified pedoclimatic zones. The Administrative Region of Campania includes several and divergent biomes, occurring close to each other. In fact, the distance between a sea level environment and that of high mountains can be less than 20 km. These environmental conditions allow the cultivation of many different crops and vegetables, represented by diverse ecotypes and varieties that are well adapted to the distribution range where they have been selected and grown. Efforts to maintain and further increase biodiversity in farming systems require a better understanding of the existing diversity created by traditional farming practices. The aim of our study was to identify and molecularly characterize several ecotypes belonging to five horticultural species commonly cultivated in Campania. In particular, we analysed five ecotypes of maize, two of garlic, four of onion, one of escarole, and two of courgette by means of simple sequence repeat (SSR) markers in order to evaluate their level of genetic biodiversity. The results reveal, for the first time, the high genetic biodiversity of horticultural ecotypes of the Campania Region. This feature is very important to improve the quality and productivity of agroecosystems.

Construction of genetic linkage map and identification of QTLs related to agronomic traits in DH population of maize (Zea mays L.) using SSR markers

BACKGROUND

In this study, we used phenotypic and genetic analysis to investigate Double haploid (DH) lines derived from normal corn parents (HF1 and 11S6169). DH technology offers an array of advantages in maize genetics and breeding as follows: first, it significantly shortens the breeding cycle by development of completely homozygous lines in two or three generations; and second, it simplifies logistics, including requiring less time, labor, and financial resources for developing new DH lines compared with the conventional RIL population development process.

OBJECTIVES

In our study, we constructed a maize genetic linkage map using SSR markers and a DH population derived from a cross of normal corn (HF1) and normal corn (11S6169).

METHODS

The DH population used in this study was developed by the following methods: we crossed normal corn (HF1) and normal corn (11S6169), which are parent lines of a normal corn cultivar, in 2014; and the next year, the F₁ hybrids were crossed with a tropicalized haploid inducer line (TAIL), which is homozygous for the dominant marker gene R1-nj (Nanda and Chase in Crop Sci 6:213-215, 1966), and we harvested seeds of the haploid lines.

RESULTS

A total of 200 SSR markers were assigned to 10 linkage groups that spanned 1145.4 cM with an average genetic distance between markers of 5.7 cM. 68 SSR markers showed Mendelian segregation ratios in the DH population at a 5% significance threshold. A total of 15 quantitative trait loci (QTLs) for plant height (PH), ear height (EH), ear height ratio (ER), leaf length (LL), ear length (EL), set ear length (SEL), set ear ratio (SER), ear width (EW), 100 kernel weight (100 KW), and cob color (CC) were found in the 121 lines in the DH population.

CONCLUSION

The results of this study may help to improve the detection and characterization of agronomic traits and provide great opportunities for maize breeders and researchers using a DH population in maize breeding programs.

Genetic diversity and population structure analysis of Indian garlic (Allium sativum L.) collection using SSR markers

Genetic diversity was assessed among 53 Indian garlic accessions using SSR markers. Initially, 24 SSR primer pairs were used for screening three selected garlic accessions. Out of 24 SSR primer pairs, 10 primer pairs which consistently showed good amplification and polymorphism were selected for DNA profiling. SSR primer pairs showed PIC values ranging from 0.30 to 0.99. Based on AMOVA we found that the greater part of the genetic diversity was expected due to intra population with 84% variation and only 16% of variation was due to among populations suggesting presence of genetic structure. The results of cluster analysis and principal component analysis largely correspond to each other. Population structure analysis revealed genetic differentiation of accessions. The results of present study revealed existence of significant variability in Indian garlic germplasm.

Genetic diversity and population structure analysis in Perilla crop and their weedy types from northern and southern areas of China based on simple sequence repeat (SSRs)

INTRODUCTION

Identification of genetic variation is an essential ability for the long-term success of breeding programs and maximizes the use of germplasm resources. In East Asia, China has a long history of the cultivation of Perilla crop, but there has been little research on the genetic diversity and genetic relationships among accessions of Perilla crop and their weedy types.

OBJECTIVES

To better understand the genetic variations of the cultivated and weedy types of Perilla crop in China, the 91 accessions were evaluated for genetic diversity by 21 simple sequence repeat (SSR) markers.

METHODS

SSR amplifications were conducted in a total volume of 20 µL, consisting of 20 ng genomic DNA, 1X PCR buffer, 0.5 µM forward and reverse primers, 0.2 mM dNTPs, and 1 U Taq polymerase. Power Marker version 3.25 was applied to obtain the information on the number of alleles, allele frequency, major allele frequency, gene diversity (GD), and polymorphic information content (PIC). The similarity matrix was used to construct an unweighted pair group method with arithmetic mean dendrogram by the application of SAHN-Clustering from NTSYS-pc.V.2.1.

RESULTS

A total of 147 alleles were identified with an average of 7 alleles per locus. The average values of PIC and GD were 0.577 and 0.537, respectively. The genetic diversity level of accessions from Northern China was lower than accessions from Southern China. The genetic diversity level and PIC values for accessions of var. crispa were the highest. For accessions of cultivated var. frutescens, genetic diversity in Southern China was higher than that in Northern China.

CONCLUSION

Most cultivated Perilla accessions were clearly separated from weedy Perilla accessions, but there was no clear geographic structure between cultivated Perilla crop and weedy types based on their regional distribution. This study demonstrated the utility of SSR analysis for performing genetic and population analysis of cultivated and weedy types of Perilla accessions in China.

Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

This study evaluated the genetic diversity and population structures in a novel cotton germplasm collection comprising 132 diploids, including Glossypium klotzschianum and allotetraploid cotton accessions, including Glossypium barbadense, Glossypium darwinii, Glossypium tomentosum, Glossypium ekmanianum, and Glossypium stephensii, from Santa Cruz, Isabella, San Cristobal, Hawaiian, Dominican Republic, and Wake Atoll islands. A total of 111 expressed sequence tag (EST) and genomic simple sequence repeat (gSSR) markers produced 382 polymorphic loci with an average of 3.44 polymorphic alleles per SSR marker. Polymorphism information content values counted 0.08 to 0.82 with an average of 0.56. Analysis of a genetic distance matrix revealed values of 0.003 to 0.53 with an average of 0.33 in the wild cotton collection. Phylogenetic analysis supported the subgroups identified by STRUCTURE and corresponds well with the results of principal coordinate analysis with a cumulative variation of 45.65%. A total of 123 unique alleles were observed among all accessions and 31 identified only in G. ekmanianum. Analysis of molecular variance revealed highly significant variation between the six groups identified by structure analysis with 49% of the total variation and 51% of the variation was due to diversity within the groups. The highest genetic differentiation among tetraploid populations was observed between accessions from the Hawaiian and Santa Cruz regions with a pairwise FST of 0.752 (p < 0.001). DUF819 containing an uncharacterized gene named yjcL linked to genomic markers has been found to be highly related to tryptophan-aspartic acid (W-D) repeats in a superfamily of genes. The RNA sequence expression data of the yjcL-linked gene Gh_A09G2500 was found to be upregulated under drought and salt stress conditions. The existence of genetic diversity, characterization of genes and variation in novel germplasm collection will be a landmark addition to the genetic study of cotton germplasm.

Genetic diversity and population structure among accessions of Perilla frutescens (L.) Britton in East Asia using new developed microsatellite markers

SSRs were successfully isolated from the Perilla crop in our current study, and used to analyze Perilla accessions from East Asia. Analyses of the clear genetic diversity and relationship for Perilla crop still remain insufficient. In this study, 40 new simple sequence repeat (SSR) primer sets were developed from RNA sequences using transcriptome analysis. These new SSR markers were applied to analyze the diversity, relationships, and population structure among 35 accessions of the two cultivated types of Perilla crop and their weedy types. A total of 220 alleles were identified at all loci, with an average of 5.5 alleles per locus and a range between 2 and 10 alleles per locus. The MAF (major allele frequency) per locus varied from 0.229 to 0.943, with an average of 0.466. The average polymorphic information content (PIC) value was 0.603, ranging from 0.102 to 0.837. The genetic diversity (GD) ranged from 0.108 to 0.854, with an average of 0.654. Based on population structure analysis, all accessions were divided into three groups: Group I, Group II and the admixed group. This study demonstrated the utility of new SSR analysis for the study of genetic diversity and population structure among 35 Perilla accessions. The GD of each locus for accessions of cultivated var. frutescens, weedy var. frutescens, cultivated var. crispa, and weedy var. crispa were 0.415, 0.606, 0.308, and 0.480, respectively. Both weedy accessions exhibited higher GD and PIC values than their cultivated types in East Asia. The new SSR primers of Perilla species reported in this study may provide potential genetic markers for population genetics to enhance our understanding of the genetic diversity, genetic relationship and population structure of the cultivated and weedy types of P. frutescens in East Asia. In addition, new Perilla SSR primers developed from RNA-seq can be used in the future for cultivar identification, conservation of Perilla germplasm resources, genome mapping and tagging of important genes/QTLs for Perilla breeding programs.

Chloroplast genomes of Lilium lancifolium, L. amabile, L. callosum, and L. philadelphicum: Molecular characterization and their use in phylogenetic analysis in the genus Lilium and other allied genera in the order Liliales

Chloroplast (cp) genomes of Lilium amabile, L. callosum, L. lancifolium, and L. philadelphicum were fully sequenced. Using these four novel cp genome sequences and five other previously sequenced cp genomes, features of the cp genomes were characterized in detail among species in the genus Lilium and other related genera in the order Liliales. The lengths and nucleotide composition showed little variation. No structural variation was found among the cp genomes in Liliales. Gene contents were conserved among four newly sequenced cp genome in Lilium species, the only differences being in two pseudogenes. We identified 112 genes in 13 functional categories, 18 of which carried introns that were conserved among the species in Liliales. There were 16-21 SSR loci (>12 bp, >3 repeats) in the cp genomes in Lilium and the genomic locations of these loci were highly variable among the species. Average mutations were 15 SNPs per 1kb and 5 indels per 1kb, respectively, in the cp genomes of the newly sequenced four Lilium species. Phylogenetic classifications revealed some discrepancies between trees based on the cp genomes and previous classifications based on the morphology and geographic distributions.

Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing

Angelica gigas Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs) are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV) of A. gigas, derived from next generation sequencing (NGS). From the putative SSR regions identified, a total of 16,496 primer sets were successfully designed. Among them, we selected 848 SSR markers that showed polymorphism from in silico analysis and contained tri- to hexa-nucleotide motifs. We tested 36 SSR primer sets for polymorphism in 16 A. gigas accessions. The average polymorphism information content (PIC) was 0.69; the average observed heterozygosity (HO) values, and the expected heterozygosity (HE) values were 0.53 and 0.73, respectively. These newly developed SSR markers would be useful tools for molecular genetics, genotype identification, genetic mapping, molecular breeding, and studying species relationships of the Angelica genus.

Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea)

Spinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected. Of these, 100 primer pairs were tested and 85% were found to yield clear, reproducible amplicons. These 85 markers were then applied to 48 spinach accessions from worldwide origins, resulting in 389 alleles with 89% polymorphism. The average gene diversity (GD) value of the markers (based on a GD calculation that ranges from 0 to 0.5) was 0.25. Our results demonstrated that the newly developed SSR markers are suitable for assessing genetic diversity and population structure of spinach germplasm. The markers also revealed clustering of the accessions based on geographical origin with clear separation of Far Eastern accessions which had the overall highest genetic diversity when compared with accessions from Persia, Turkey, Europe, and the USA. Thus, the SSR markers have good potential to provide valuable information for spinach breeding and germplasm management. Also they will be helpful for genome mapping and core collection establishment.

Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)

Single nucleotide polymorphisms (SNPs) are widely used in genetics and genomics research. The Pacific oyster (Crassostrea gigas) is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an oyster 190K SNP array using Affymetrix Axiom genotyping technology. We designed 190,420 SNPs on the chip; these SNPs were selected from 54 million SNPs identified through re-sequencing of 472 Pacific oysters collected in China, Japan, Korea, and Canada. Our genotyping results indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. The SNPs were distributed evenly throughout the oyster genome, located in 3,595 scaffolds with a length of ~509.4 million; the average interval spacing was 4,210 bp. In addition, 111,158 SNPs were distributed in 21,050 coding genes, with an average of 5.3 SNPs per gene. In comparison with genotypes obtained through re-sequencing, ~69% of the converted SNPs had a concordance rate of >0.971; the mean concordance rate was 0.966. Evaluation based on genotypes of full-sib family individuals revealed that the average genotyping accuracy rate was 0.975. Carrying 133 K polymorphic SNPs, our oyster 190K SNP array is the first commercially available high-density SNP chip for mollusks, with the highest throughput. It represents a valuable tool for oyster genome-wide association studies, fine linkage mapping, and population genetics.

Microsatellite (SSR) amplification by PCR usually led to polymorphic bands: Evidence which shows replication slippage occurs in extend or nascent DNA strands

Microsatellites or simple sequence repeats (SSRs) are very effective molecular markers in population genetics, genome mapping, taxonomic study and other large-scale studies. Variation in number of tandem repeats within microsatellite refers to simple sequence length polymorphism (SSLP); but there are a few studies that are showed SSRs replication slippage may be occurred during in vitro amplification which are produced 'stutter products' differing in length from the main products. The purpose of this study is introducing a reliable method to realize SSRs replication slippage. At first, three unique primers designed to amplify SSRs loci in the great gerbil (Rhombomys opimus) by PCR. Crush and soak method used to isolate interesting DNA bands from polyacrylamide gel. PCR products analyzed using by sequencing methods. Our study has been shown that Taq DNA polymerase slipped during microsatellite in vitro amplification which led to insertion or deletion of repeats in sense or antisense DNA strands. It is produced amplified fragments with various lengths in gel electrophoresis showed as 'stutter bands'. Thus, in population studies by SSRs markers recommend that replication slippage effects and stutter bands have been considered.

Ribosomal DNA locus variation and REMAP analysis of the diploid and triploid complexes of Lilium lancifolium

Lilium lancifolium Thunb. (2n = 2x = 24) is a cytologically conspicuous species with both diploids and triploids in nature. Cytological and molecular genetic analyses were carried out in both diploids and triploids that were collected from 55 geographical locations in Korea, Japan, and China. While the 5S rRNA gene loci were located at duplicated loci on the long arm of chromosome 2, the 45S rRNA gene loci were present in chromosomes 1, 2, 4, 6, 7, and 11. While the loci on chromosomes 1 and 7 were constant, the loci on chromosomes 2, 4, 6, 7, and 11 were variable in some plants so that the L. lancifolium accessions were grouped into 7 cytotypes in diploids and 12 cytotypes in triploids. REMAP marker analysis revealed that the diploids were classified into seven clusters, and the triploids were classified into a large cluster. Geographic, cytological, and genetic differentiations were not related in both the diploid and triploid accessions of L. lancifolium. Thus, current genetic variations occurred prior to the geographic differentiation in both diploids and triploids, and the 45S rDNA cytotype variations occurred after geographic differentiation in the current habitats of L. lancifolium.

Isolation and characterization of genomic microsatellite markers for small cardamom (Elettaria cardamomum Maton) for utility in genetic diversity analysis

Microsatellite markers in small cardamom (Elettaria cardamomum Maton) were developed using the selective hybridization enrichment method. A total of 140 microsatellite repeats were identified from 270 clones. Primers were designed for 58 microsatellites and 44 primer pairs amplified products of expected size in cardamom. These markers were used for studying the diversity of 20 important small cardamom genotypes, and six markers were found to be polymorphic. The number of alleles ranged from 2 to 7 with an average of 3.6 per locus. Polymorphic information content values ranged from 0.14 to 0.38 based on dominant scoring. The two markers ECM 47a and ECMG 28 generated specific banding patterns for the genotypes MCC7 (Pink tiller) and APG434 (MA18) respectively. Dendrogram illustrated the genetic similarity between different genotypes of Kerala and Karnataka regions. It differentiated the closely related genotypes and released varieties into separate groups. Principal coordinate analysis revealed PV1 and ICRI 1 as the most divergent genotypes. The study demonstrated that these markers are informative and can be further utilized for generating reliable molecular data for assisting the crop improvement of small cardamom. Cross generic transferability (71.4 %) of the developed primers proved that they are useful for phylogenetic studies in the family Zingiberaceae. This is the first report of de novo isolation, characterisation and utilization of microsatellite markers for the genetic diversity analysis of small cardamom.

Microsatellites in Pursuit of Microbial Genome Evolution

Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.

Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food

In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.

Candidate Gene Polymorphisms and their Association with Glycogen Content in the Pacific Oyster Crassostrea gigas

BACKGROUND

The Pacific oyster Crassostrea gigas is an important cultivated shellfish that is rich in nutrients. It contains high levels of glycogen, which is of high nutritional value. To investigate the genetic basis of this high glycogen content and its variation, we conducted a candidate gene association analysis using a wild population, and confirmed our results using an independent population, via targeted gene resequencing and mRNA expression analysis.

RESULTS

We validated 295 SNPs in the 90 candidate genes surveyed for association with glycogen content, 86 of were ultimately genotyped in all 144 experimental individuals from Jiaonan (JN). In addition, 732 SNPs were genotyped via targeted gene resequencing. Two SNPs (Cg_SNP_TY202 and Cg_SNP_3021) in Cg_GD1 (glycogen debranching enzyme) and one SNP (Cg_SNP_4) in Cg_GP1 (glycogen phosphorylase) were identified as being associated with glycogen content. The glycogen content of individuals with genotypes TT and TC in Cg_SNP_TY202 was higher than that of individuals with genotype CC. The transcript abundance of both glycogen-associated genes was differentially expressed in high glycogen content and low glycogen content individuals.

CONCLUSIONS

This study identified three polymorphisms in two genes associated with oyster glycogen content, via candidate gene association analysis. The transcript abundance differences in Cg_GD1 and Cg_GP1 between low- and the high-glycogen content individuals suggests that it is possible that transcript regulation is mediated by variations of Cg_SNP_TY202, Cg_SNP_3021, and Cg_SNP_4. These findings will not only provide insights into the genetic basis of oyster quality, but also promote research into the molecular breeding of oysters.