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.

Toxic effects of lead on plants: integrating multi-omics with bioinformatics to develop Pb-tolerant crops.

MAIN CONCLUSION: Lead disrupts plant metabolic homeostasis and key structural elements. Utilizing modern biotechnology tools, it's feasible to develop Pb-tolerant varieties by discovering biological players regulating plant metabolic pathways under stress. Lead (Pb) has been used for a variety of purposes since antiquity despite its toxic nature. After arsenic, lead is the most hazardous heavy metal without any known beneficial role in the biological system. It is a crucial inorganic pollutant that affects plant biochemical and morpho-physiological attributes. Lead toxicity harms plants throughout their life cycle and the extent of damage depends on the concentration and duration of exposure. Higher levels of lead exposure disrupt numerous key metabolic activities of plants including oxygen-evolving complex, organelles integrity, photosystem II connectivity, and electron transport chain. This review summarizes the detrimental effects of lead toxicity on seed germination, crop growth, and yield, oxidative and ultra-structural alterations, as well as nutrient absorption, transport, and assimilation. Further, it discusses the Pb-induced toxic modulation of stomatal conductance, photosynthesis, respiration, metabolic-enzymatic activity, osmolytes accumulation, and antioxidant activity. It is a comprehensive review that reports on omics-based studies along with morpho-physiological and biochemical modifications caused by lead stress. With advances in DNA sequencing technologies, genomics and transcriptomics are gradually becoming popular for studying Pb stress effects in plants. Proteomics and metabolomics are still underrated and there is a scarcity of published data, and this review highlights both their technical and research gaps. Besides, there is also a discussion on how the integration of omics with bioinformatics and the use of the latest biotechnological tools can aid in developing Pb-tolerant crops. The review concludes with core challenges and research directions that need to be addressed soon.

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.

Efficacy of Carbon Nanodots and Manganese Ferrite (MnFe2O4) Nanoparticles in Stimulating Growth and Antioxidant Activity in Drought-Stressed Maize Inbred Lines.

Despite being the third most-consumed crop, maize (Zea mays L.) is highly vulnerable to drought stress. The predominant secondary metabolite in plants is phenolic acids, which scavenge reactive oxygen species to minimize oxidative stress under drought stress. Herein, the effect of carbon nanodots (CND) and manganese ferrite (MnFe2O4) nanoparticles (NP) on the drought stress tolerance of maize has been studied. The experimental results revealed that the highest leaf blade length (54.0 cm) and width (3.9 cm), root length (45.2 cm), stem diameter (11.1 mm), root fresh weight (7.0 g), leaf relative water content (84.8%) and chlorogenic (8.7 µg/mL), caffeic (3.0 µg/mL) and syringic acid (1.0 µg/mL) contents were demonstrated by CND-treated (10 mg L-1) inbred lines (GP5, HW19, HCW2, 17YS6032, HCW3, HCW4, HW7, HCW2, and 16S8068-9, respectively). However, the highest shoot length (71.5 cm), leaf moisture content (83.9%), shoot fresh weight (12.5 g), chlorophyll content (47.3), and DPPH free radical scavenging activity (34.1%) were observed in MnFe2O4 NP-treated (300 mg L-1) HF12, HW15, 11BS8016-7, HW15, HW12, and KW7 lines, respectively. The results indicate that CND and MnFe2O4 NP can mitigate drought stress effects on different accessions of the given population, as corroborated by improvements in growth and physio-biochemical traits among several inbred lines of maize.

Spodoptera frugiperda (Lepidoptera: Noctuidae) Life Table Comparisons and Gut Microbiome Analysis Reared on Corn Varieties.

The fall armyworm (Spodoptera frugiperda, FAW) is an invasive migratory pest that has recently spread to Korea, damaging several corn cultivars with significant economic value. Comparisons of the growth stages of FAW were conducted based on the preferred feed. Therefore, we selected six maize cultivars, including three categories: (i) commercial waxy corn (mibaek 2-ho, heukjeom 2-ho, dreamoak); (ii) popcorn (oryun popcorn, oryun 2-ho); and (iii) processing corn (miheukchal). A significant effect was observed during the larvae period, pupal period, egg hatching ratio, and larvae weight, whereas the total survival period and adult period did not show significant variation among the tested corn cultivars. We identified variations in the FAW gut bacterial community that were dependent on the genotype of the corn maize feed. The identified phyla included Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Among these genera, the most abundant bacterial genus was Enterococcus, followed by Ureibacillus. Enterococcus mundtii was the most abundant among the top 40 bacterial species. The intergenic PCR-based amplification and gene sequence of the colony isolates were also matched to the GenBank owing to the prevalence of E. mundtii. These results showed that the bacterial diversity and abundance of particular bacteria in the guts of FAWs were influenced by the six major maize corn cultivars.

Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers.

The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. The average value of amylose content for an 80-recombinant-inbred-line (RIL) population was 8.8 ± 0.7%, ranging from 2.1 to 15.9%. We used two different analyses-Q + K and PCA + K mixed linear models (MLMs)-and found 38 (35 SNP and 3 SSR) and 32 (29 SNP and 3 SSR) marker-trait associations (MTAs) associated with amylose content. A total of 34 (31 SNP and 3 SSR) and 28 (25 SNP and 3 SSR) MTAs were confirmed in the Q + K and PCA + K MLMs, respectively. This study detected some candidate genes for amylose content, such as GRMZM2G118690-encoding BBR/BPC transcription factor, which is used for the control of seed development and is associated with the amylose content of rice. GRMZM5G830776-encoding SNARE-interacting protein (KEULE) and the uncharacterized marker PUT-163a-18172151-1376 were significant with higher R2 value in two difference methods. GRMZM2G092296 were also significantly associated with amylose content in this study. This study focused on amylose content using a RIL population derived from dent and waxy inbred lines using molecular markers. Future studies would be of benefit for investigating the physical linkage between starch synthesis genes using SNP and SSR markers, which would help to build a more detailed genetic map and provide new insights into gene regulation of agriculturally important traits.

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 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.

Mapping of QTL for agronomic traits using high-density SNPs with an RIL population in maize.

BACKGROUND: Genome wide association studies (GWAS) have been widely used to identify QTLs underlying quantitative traits in humans and animals, and they have also become a popular method of mapping QTLs in many crops, including maize. Advances in high-throughput genotyping technologies enable construction of high-density linkage maps using SNP markers. OBJECTIVES: High-density genetic mapping must precede to find molecular markers associated with a particular trait. The objectives of this study were to (1) construct a high-density linkage map using SNP markers and (2) detect the QTLs for grain yield and quality related traits of the Mo17/KW7 RIL population. METHODS: In this study, two parental lines, Mo17 (normal maize inbred line) and KW7 (waxy inbred line) and 80 F7:8 lines in the Mo17/KW7 RIL population were genotyped using the MaizeSNP50 BeadChip, an Illumina BeadChip array of 56,110 maize SNPs. Marker integration and detection of QTLs was performed using the inclusive composite interval mapping (ICIM) method within the QTL IciMapping software. RESULTS: This study was genotyped using the Illumina MaizeSNP50 BeadChip for maize Mo17/KW7 recombinant inbred line (RIL) population. The 2904 SNP markers were distributed along all 10 maize chromosomes. The total length of the linkage map was 3553.7 cm, with an average interval of 1.22 cm between SNPs. A total of 18 QTLs controlling eight traits were detected in the Mo17/KW7 RIL population. Three QTLs for plant height (PH) were detected on chromosomes 4 and 8 and showed from 16.01% (qPH8) to 19.85% (qPH4a) of phenotypic variance. Five QTLs related to ear height (EH) were identified on chromosomes 3, 4, and 6 and accounted for 3.79% (qEH6) to 27.57% (qEH4b) of phenotypic variance. Five QTLs related to water content (WC) on chromosomes 1, 4, 8, and 9 accounted for 9.55% (qWC8b) to 23.30% (qWC4) of phenotypic variance. One QTL (qAC9) relating to amylose content (AC) on chromosome 9 showed 82.10% of phenotypic variance. CONCLUSIONS: The high-density linkage map and putative QTLs of the maize RIL population detected in this study can be effectively utilized in waxy and normal maize breeding programs to facilitate the selection process through marker-assisted selection (MAS) breeding programs.

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.

Bulk segregant analysis identifies SSR markers associated with leaf- and seed-related traits in Perilla crop (Perilla frutescens L.).

BACKGROUND: Bulk segregant analysis (BSA) is another method of identifying significant molecular markers linked to the target gene or region for specific traits. BSA is easier and less expensive than other methods; it does not require genetic map construction and needs fewer markers than the number needed to construct a genetic map for QTL mapping. OBJECTIVES: The purpose of our study was to identify simple sequence repeat (SSR) markers linked with leaf- and seed-related traits in Perilla crop, and to allow the selection of better accessions in Perilla breeding programs with marker-assisted selection (MAS). METHODS: The genotypes of the 25 SSR markers and phenotypic data for the eight qualitative traits were used to confirm significant marker-trait associations (SMTAs) using TASSEL software. To detect SSR markers associated with leaf color, the 16 individuals of the F3 population were divided into three bulk groups based on the colors of the surface and reverse sides of the leaf, respectively: six in the green/green group, five in the green/purple group and five in the purple/purple group. RESULTS: This study detected 18 significant marker-trait associations (SMTAs) involving 12 SSR markers associated with six agronomic traits. The SSR markers KNUPF15, KNUPF21, KNUPF29, and KNUPF60 were associated with leaf surface color, and KNUPF11, KNUPF15, KNUPF21, and KNUPF60 were associated with leaf reverse side color. In addition, five SSR markers were associated with seed-related traits. KNUPF11 and KNUPF29 were associated with seed coat color, while KNUPF29 was associated with seed size. KNUPF12, KNUPF16, and KNUPF42 were associated with seed hardness. To verify the selected significant SSR markers associated with leaf color and seed-related traits, a UPGMA dendrogram for 11 individuals in the F3 population, which formed two bulk groups consisting of 6 green/green and 5 purple/purple individuals, was constructed using six SSR marker-related LC and RLC traits. CONCLUSION: These results are very important for understanding the characteristics of Perilla leaves and seeds; they may also support opportunities to effectively preserve and utilize existing accessions and to allow Perilla breeders to improve crop quality by mean of MAS.

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.

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.

The comparative gene expression concern to the seed pigmentation in maize (Zea mays L.).

Maize seed pigmentation is one of the important issue to develop maize seed breeding. The differently gene expression was characterized and compared for three inbred lines, such as the pigment accumulated seed (CM22) and non-pigmented seed (CM5 and CM19) at 10 days after pollination. We obtained a total of 63,870, 82,496, and 54,555 contigs by de novo assembly to identify gene expression in the CM22, CM5, and CM19, respectably. In differentially expressed gene analysis, it was revealed that 7,044 genes were differentially expressed by at least two-fold, with 4,067 upregulated in colored maize inbred lines and 2,977 upregulated in colorless maize inbred lines. Of them,18 genes were included to the anthocyanin biosynthesis pathways, while 15 genes were upregulated in both CM22/5 and CM22/19. Additionally, 37 genes were detected in the metabolic pathway concern to the seed pigmentation by BINs analysis using MAPMAN software. Finally, these differently expressed genes may aid in the research on seed pigmentation in maize breeding programs.

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.

Genetic differentiation of Mutator insertion polymorphisms and association with agronomic traits in waxy and common maize.

BACKGROUND: As waxy maize is considered a key economic crop in Korea, an understanding of its genetic variation and differentiation is fundamental for the selective plant breeding. The maize genome is primarily composed of transposable elements, for which large and stable insertions generate variations that reflect selection during evolution. OBJECTIVES: This study was to elucidate the genetic diversity based on the contribution of TEs and to investigate the effect of Mu transposition on the genetic divergence of waxy and common maize. We also performed an association analysis on these inbred lines to determine the Mu insertions associated with agronomic traits. METHODS: In this study, we utilized a Mutator-based transposon display method to study the genetic diversity and population structure of 40 waxy and 40 common inbred lines of maize in the Gangwon Agricultural Research and Extension Services collection at the Maize Research Institute. RESULTS: We detected polymorphisms in 86.33% of 278 Mutator (Mu) anchored loci, reflecting the activity of the Mu element and its contribution to genetic variation. Common maize showed a substantial amount of genetic diversity, which was greater than that observed in waxy maize. Principal-coordinate and neighbor-joining cluster analyzes consistently supported the presence of two genetically distinct groups. However, the distribution of genetic variation within the populations was much higher than the genetic differentiation among the populations. To explore the contribution of the Mu element to phenotypic variation, we analyzed the associations with ten important agronomical traits. On the basis of the combined results from two models (QGLM and Q + KLM), we found significant associations between seven Mu loci and four different traits. CONCLUSIONS: These results will assist waxy maize breeders in choosing parental lines and be useful for marker-assisted selection.

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.