A Comprehensive Genome-Wide Association Study of Carotenoid and Capsaicinoid Contents in Capsicum chinense Germplasm.

Pepper is a highly important vegetable globally, both economically and nutritionally. However, to efficiently select and identify genetic resources for pepper breeding programs, it is crucial to understand the association between important traits and genetic factors. In this study, we investigated the genetic basis of carotenoid and capsaicinoid content in 160 Capsicum chinense germplasms. The study observed significant variability in carotenoid and capsaicinoid content among the germplasms. Correlation analysis revealed a strong positive correlation between violaxanthin and antheraxanthin. In contrast, capsaicin and dihydrocapsaicin displayed negative correlations with individual carotenoids but exhibited a strong positive correlation between the two compounds (r = 0.90 ***). Genotyping-by-sequencing (GBS) was performed on 160 genotypes of pepper germplasm, which identified 47,810 high-quality SNPs. A comprehensive genome-wide association analysis was performed using these SNPs to identify SNPs associated with carotenoids and capsaicinoids, revealing 193 SNPs that exhibited significant associations. Specifically, 4 SNPs were associated with violaxanthin, 2 with antheraxanthin, 86 with capsorubin, 5 with capsanthin, 63 with zeaxanthin, 3 with ß-cryptoxanthin, and 2 with α-carotene. With further studies, the significantly associated SNPs identified in this study have the potential to be utilized for selecting pepper accessions with high carotenoid and capsaicinoid contents. Additionally, the genes associated with these significant SNPs will be used to understand their roles and involvement in the biosynthesis pathway of carotenoids and capsaicinoids. Understanding the function of these genes can provide insights into the molecular mechanisms underlying the production of these bioactive compounds in pepper. The findings of this study hold valuable implications for selecting pepper varieties with desirable traits and developing breeding programs aimed at enhancing the nutritional and medicinal properties of pepper.

Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing.

Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.

Novel microsatellite markers acquired from Rubus coreanus Miq. and cross-amplification in other Rubus species.

The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3%) type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%). The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry). These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.

Cross-amplification of Vicia sativa subsp. sativa microsatellites across 22 other Vicia species.

The temperate and herbaceous genus Vicia L. is a member of the legume tribe Fabeae of the subfamily Papilionoideae. The genus Vicia comprises 166 annual or perennial species distributed mainly in Europe, Asia, and North America, but also extending to the temperate regions of South America and tropical Africa. The use of simple sequence repeat (SSR) markers for Vicia species has not been investigated as extensively as for other crop species. In this study, we assessed the potential for cross-species amplification of cDNA microsatellite markers developed from common vetch (Vicia sativa subsp. sativa). For cross-species amplification of the SSRs, amplification was carried out with genomic DNA isolated from two to eight accessions of 22 different Vicia species. For individual species or subspecies, the transferability rates ranged from 33% for V. ervilia to 82% for V. sativa subsp. nigra with an average rate of 52.0%. Because the rate of successful SSR marker amplification generally correlates with genetic distance, these SSR markers are potentially useful for analyzing genetic relationships between or within Vicia species.

Exploring Disease Resistance in Pepper (Capsicum spp.) Germplasm Collection Using Fluidigm SNP Genotyping.

This study utilized a diverse Capsicum accessions (5658) sourced from various species and geographical regions, deposited at the National Agrobiodiversity Center, Genebank. We employed 19 SNP markers through a Fluidigm genotyping system and screened these accessions against eight prevalent diseases of pepper. This study revealed accessions resistant to individual diseases as well as those exhibiting resistance to multiple diseases, including bacterial spot, anthracnose, powdery mildew, phytophthora root rot, and potyvirus. The C. chacoense accessions were identified as resistant materials against bacterial spot, anthracnose, powdery mildew, and phytophthora root rot, underscoring the robust natural defense mechanisms inherent in the wild Capsicum species and its potential uses as sources of resistance for breeding. C. baccatum species also demonstrated to be a promising source of resistance to major pepper diseases. Generally, disease-resistant germplasm has been identified from various Capsicum species. Originating from diverse locations such as Argentina, Bolivia, and the United Kingdom, these accessions consistently demonstrated resistance, indicating the widespread prevalence of disease-resistant traits across varied environments. Additionally, we selected ten pepper accessions based on their resistance to multiple diseases, including CMV, Phytophthora root rot, potyviruses, and TSWV, sourced from diverse geographical regions like Hungary, Peru, the United States, and the Netherlands. This comprehensive analysis provides valuable insights into disease resistance in Capsicum, crucial for fostering sustainable agricultural practices and advancing crop improvement through breeding strategies.

Associations of the Seed Fatty Acid Composition of Sesame (Sesamum indicum L.) Germplasm with Agronomic Traits and FAD2 Variations.

Sesame is an important oilseed crop grown for human consumption in many countries, with a high commercial value due to its high oleic/linoleic acid ratio (O/L ratio). However, its properties may vary among different accessions. In the current study, 282 sesame accessions were evaluated to determine the effects of agronomic traits and genotypes on the O/L ratio. The O/L ratio was positively correlated with the oleic acid (C18:1), stearic acid (C18:0), and myristic acid (C14:0) concentrations, as well as the capsule zone length (CZL), capsule width (CW), and capsule length (CL), and negatively correlated with the linoleic acid (C18:2) and linolenic acid (C18:3) concentrations, the days to maturity (DTM), days to flowering (DTF), and the height of the first capsule-bearing node (HFC) (p < 0.05). In addition, the O/L ratio was affected by the FAD2 haplotype, as the Hap2 and Hap3 sesame accessions had lower O/L ratios. Therefore, we suggest that the increase and decrease in the contents of C18:1 and C18:2 are associated with the FAD2 haplotype. A total of 25 agronomic traits and fatty acid compositions were compared via statistical analysis, and accessions with a high O/L ratio were selected. The results of this study can be used as a basis for further research on the development of new sesame varieties through enhancing nutritional functionality.

Quantification and Diversity Analyses of Major Glucosinolates in Conserved Chinese Cabbage (Brassica rapa L. ssp. pekinensis) Germplasms.

The genebank at the National Agrobiodiversity Center (RDA-Genebank, Jeonju, Republic of Korea), conserves approximately 8000 germplasms of Brassica spp., of which Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the major crops actively used as food in Northeast Asia, including Korea, as the main ingredient for kimchi. Glucosinolates are a major class of compounds in Chinese cabbage that are responsible for their distinctive flavor, and RDA-Genebank is constantly building a related database (DB) to select suitable germplasms required by consumers and provide resources for breeding programs. In this study, ten glucosinolates were analyzed in sixty Chinese cabbage germplasms. Six aliphatic glucosinolates were the major components, accounting for 85.00% to 91.98% of total glucosinolates in each germplasm. Among them, gluconapin (333.26 to 23,501.58 µmol∙kg-1 DW) was highly represented, followed by glucobrassicanapin (545.60 to 10,344.70 µmol∙kg-1 DW) and progoitrin (155.28 to 8536.51 µmol∙kg-1 DW). In addition, we selected germplasms with a high content of each studied glucosinolate. To analyze the diversity and distribution of glucosinolates among the studied germplasms, Pearson's correlation was performed, and the related results were interpreted through their biosynthetic pathways. The k-means clustering indicated four optimal clusters, which were confirmed through principal component analysis. Orthogonal projection to latent structure discriminant analysis (OPLS-DA) was also performed on the status (landrace and cultivar) and origin (Korea, China, Taiwan, and Japan) passport data of the germplasms, followed by the calculation of variable importance in the projection (VIP) values. These results are part of a continuous series of studies to analyze the glucosinolates of Brassica germplasms that are being conserved at RDA-Genebank. We aim to provide related results through a public platform accessible to everyone and thereby improve the distribution of Brassica germplasms.

Distinct Effects of Seed Coat and Flower Colors on Metabolite Contents and Antioxidant Activities in Safflower Seeds.

Safflower is an important oilseed crop cultivated primarily for its seeds, which have pharmaceutical properties. Color is an important agronomical trait that appears to be a prior parameter for evaluating the internal quality of plant seeds. This study employs 197 safflower accessions seeds to analyze how their seed coat and flower colors affect their total oil content, fatty acid composition, total phenolic content (TPC), N-(p-coumaroyl)serotonin (CS) and N-feruloylserotonin (FS) contents, and [2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)] radical scavenging activities. Significant variations were observed in the targeted metabolite contents and antioxidant properties among genotypes. Notably, the linoleic acid content, total unsaturated fatty acid content, the ratio of total unsaturated fatty acid to total saturated fatty acid, CS, FS, ABTS, and DPPH scavenging capacities varied significantly based on seed coat color, with white-seeded genotypes having the highest average values of these parameters. Moreover, the linoleic acid content differed significantly (p < 0.05) among the genotypes with varying flower colors, with white-flowered accessions having the highest average content. Furthermore, genotypes K185105 (No. 75) and K175278 (No. 146) were identified as promising genetic resources with health benefits. Overall, these findings reveal that seed coat and flower colors distinctly affect metabolite contents and antioxidant properties in safflower seeds.

Evaluation of Agricultural Traits, Phytochemical Contents, and Antioxidant Activities in the Leaves of Amaranth Accessions of Nine Species.

Amaranthus species are widely cultivated as dietary crops and are promising sources of phytochemical compounds with antioxidant properties. To explore Amaranthus as a potential medical resource, 289 accessions (nine species) were cultivated, and their agricultural characteristics, total phenolic content (TPC), rutin contents, and antioxidant activities [2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)] were studied. Wide variations in agricultural traits, phytochemical contents, and antioxidant activities were observed between the accessions and across species. The effects of agricultural traits were evaluated, and the results indicated that yellow-flowered amaranth genotypes could be important because of their high values of TPC, rutin contents, DPPH, and ABTS. In addition, leaf length, days until 50% flowering, days until 50% heading and days until maturity, showed positive correlations with TPC, rutin contents, DPPH, and ABTS. The whole dataset was subjected to principal component analysis, and distinctive aggregation was observed across the Amaranthus species. In total, 289 accessions were clustered into three groups, and seven genotypes were determined as being good medical resources due to their high phytochemical content and antioxidant activities. Our findings provide important information for the development of new varieties with high phytochemical contents and high levels of antioxidant activity.

Seed Weight and Genotype Influence the Total Oil Content and Fatty Acid Composition of Peanut Seeds.

Peanut, an important oilseed crop cultivated worldwide as a dietary food, is a good food source with health benefits. To explore the potential benefits of peanuts as a food resource, 301 peanut accessions were evaluated to determine the effect of seed weight and genotype on total oil content and fatty acid composition. Total oil was extracted using the Soxhlet method and fatty acids were analyzed by gas chromatography mass spectrometry. Wide variations in the 100-seed weight, total oil content, and fatty acid profile were observed among genotypes and accession types. An effect of seed weight on the fatty acid composition of peanut seeds was observed. Increases in the oleic acid content and decreases in the linoleic acid content occurred in association with increases in the 100-seed weight. Moreover, the 100-seed weight, total oil content, and individual and total fatty acid contents, except arachidic acid, differed significantly (p < 0.001 or 0.05) among the accession types of landrace, cultivar, breeding line, and unknown. The discovery of this high diversity could contribute to further studies of peanut domestication and evolutionary classification. Our findings are important for the selection of peanut seeds with health benefits and development of new varieties of peanut with health benefits.

Classification of 17 species Aegilops using DNA barcoding and SNPs, reveals gene flow among Aegilops biuncialis, Aegilops juvenalis, and Aegilops columnaris.

Rapid changes in agricultural environments caused by global warming pose a major challenge to food production and safety. Common wheat (Triticum aestivum) is a hexaploid plant (AABBDD) that shares large numbers of quantitative traits and resistance genes with B and D genomes of Aegilops species, which are responsible for several metabolic functions and biosynthetic processes, particularly in plant adaptation to biotic as well as abiotic stresses. Comparatively, the abundance of the Aegilops gene pool is much higher than that of Triticum. Therefore, we used four universal DNA barcodes for plants (ITS2, matK, rbcL, and psbM-petN) to construct a phylogenetic tree to classify the genus Aegilops. Fourteen species were distinguished among a total of 17 representative species. Aegilops biuncialis, Aegilops juvenalis, and Aegilops umbellulata could not be grouped into any of the clusters in the phylogenetic tree, indicating that these three species could not be distinguished by four DNA barcodes. Therefore, from 2408 SNPs obtained using genotyping by sequencing (GBS), we manually screened 30 SNPs that could be potentially used to classify these three species. The results of gene flow and genetic differentiation index (Fst) showed that the genetic differentiation among the three species was small, and there was bidirectional horizontal gene transfer between the three species, which was consistent with our results that the three species were difficult to classify by DNA barcode.

Genetic Diversity and Population Structure of Potato Germplasm in RDA-Genebank: Utilization for Breeding and Conservation.

Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries. It is of critical importance to understand the genetic diversity and population structure for effective collection, conservation, and utilization of potato germplasm. Thus, the objective of the present study was to investigate the genetic diversity and population structure of potato germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea to provide basic data for future preservation and breeding of potato genetic resources. A total of 24 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 482 potato accessions. A total of 257 alleles were detected, with an average of 10.71 alleles per locus. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual accessions within the population, while only 3% was distributed among populations. Results of genetic structure analysis based on STRUCTURE and discriminant analysis of principal components revealed that 482 potato accessions could be divided into two main subpopulations. Accessions of subpopulation 1 mainly belonged to cultivars and breeding lines. Accessions of subpopulations 2 basically corresponded to wild relatives of potatoes. Results of this study provide useful information for potato improvement and conservation programs, although further studies are needed for a more accurate evaluation of genetic diversity and phenotypic traits of potatoes.

Phytochemicals and Antioxidant Activity of Korean Black Soybean (Glycine max L.) Landraces.

Black soybean (Glycine max L.) has been used as a traditional medicine because its seed coat contains various natural phenolic compounds such as anthocyanins. The objective of this study was to reveal the genetic variation in the agricultural traits, phytochemicals, and antioxidant activity of 172 Korean black soybean landraces (KBSLs) and establish a relationship among them. The evaluation of three agricultural traits (days to 50% flowering, maturity, and 100-seed weight), six phytochemicals (delphinidin-3-glucoside, cyaniding-3-glucoside, petunidin-3-glucoside, daidzin, glycitin, and genestin), and four antioxidant activities (2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid)(ABTS), ferric-reducing antioxidant power (FRAP), and the total polyphenol content (TPC) of 172 KBSLs were analyzed in 2012 and 2015. The agricultural traits, phytochemicals, and antioxidant activities of the 172 KBSLs showed wide variation among the accessions and years. In correlation analysis, the agricultural traits and phytochemicals showed positive and negative correlations with phytochemicals and antioxidant activity, respectively. The principal component analyses result indicated that phytochemicals accounted for most of the variability in the KBSLs. In clustering analysis, the 172 KBSLs were classified into four clusters. These results could lead to expanding the knowledge of the agricultural traits, phytochemicals, and antioxidant activity of the KBSLs, which are valuable materials for the development of new soybean varieties.

Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae).

Wheat (Triticum spp.) has been an important staple food crop for mankind since the beginning of agriculture. The genus Triticum L. is composed of diploid, tetraploid, and hexaploid species, majority of which have not yet been discriminated clearly, and hence their phylogeny and classification remain unresolved. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows us to generate genome-wide single nucleotide polymorphism (SNP) markers. In this study, we used GBS to obtain SNPs covering all seven chromosomes from 283 accessions of Triticum-related genera. After filtering low-quality and redundant SNPs based on haplotype information, the GBS assay provided 14,188 high-quality SNPs that were distributed across the A (71%), B (26%), and D (2.4%) genomes. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish six distinct groups that matched well with Triticum species complexity. We constructed a Bayesian phylogenetic tree using 14,188 SNPs, in which 17 Triticum species and subspecies were discriminated. Dendrogram analysis revealed that the polyploid wheat species could be divided into groups according to the presence of A, B, D, and G genomes with strong nodal support and provided new insight into the evolution of spelt wheat. A total of 2,692 species-specific SNPs were identified to discriminate the common (T. aestivum) and durum (T. turgidum) wheat cultivar and landraces. In principal component analysis grouping, the two wheat species formed individual clusters and the SNPs were able to distinguish up to nine groups of 10 subspecies. This study demonstrated that GBS-derived SNPs could be used efficiently in genebank management to classify Triticum species and subspecies that are very difficult to distinguish by their morphological characters.

Development of SSR markers for studies of diversity in the genus Fagopyrum.

The numbers of SSR markers and their utilization have not been determined and investigated as extensively in Fagopyrum species as compared to other crop species. The current report presents 136 new SSR markers in Fagopyrum esculentum ssp. esculentum and their application to related species in the genus Fagopyrum. Of the 136 SSRs, 10 polymorphic SSR markers were utilized in a genetic diversity analysis of a common buckwheat population consisting of 41 accessions of diverse origin. The study showed observed (H(O)) and expected (H(E)) heterozygosities ranging from 0.071 to 0.924 (mean = 0.53) and from 0.073 to 0.902 (mean = 0.412), respectively. Forty-one of the 136 SSRs amplified sequences in other Fagopyrum species, including the cymosum and urophyllum groups. The phylogenetic relationships revealed using the SSRs was consistent with results obtained using other marker systems, with one exception. The sequence and diversity information obtained using these new SSRs and their cross-transferability to related Fagopyrum species will increase our understanding of genetic structures and species relationships within the Fagopyrum genus.

Development and characterization of new microsatellite markers for the oyster mushroom (Pleurotus ostreatus).

We developed and characterized 36 polymorphic microsatellite markers for the oyster mushroom (Pleurotus ostreatus). In total, 169 alleles were identified with an average of 4.7 alleles per locus. Values for observed (HO) and expected (HE) heterozygosities ranged from 0.027 to 0.946 and from 0.027 to 0.810, respectively. Nineteen loci deviated from Hardy-Weinberg equilibrium. Significant (P<0.05) excess heterozygosity was observed at nine loci. Linkage disequilibrium (LD) was significant (P<0.05) between pairs of locus alleles. Cluster analysis revealed that five species of genus Pleurotus made a distinct group, and the individual cultivars were grouped into major five groups from G-1 to G-5. The diverse cultivars of P. ostreatus were discriminated and the other four species revealed a different section in the UPGMA tree. These microsatellite markers proved to be very useful tools for genetic studies, including assessment of the diversity and population structure of P. ostreatus.

The complete chloroplast genome sequence of wild oat, Avena sterilis L. (Poaceae) and its phylogeny.

Wild oat, Avena sterilis L. is a stout broad-leaved annual grass resembling cultivated oats in general appearance. In this study, we sequenced the complete chloroplast (cp) genome sequence of A. sterilis for the first time to investigate their phylogenetic relationship in the family Poaceae. The complete cp genome sequence is 135,887 bp in length with 38.5% overall GC content and exhibits a typical quadripartite structure comprising one pair of inverted repeats (21,603 bp) separated by a small single-copy region (12,575 bp) and a large single-copy region (80,106). The cp genome encodes 111 unique genes, 76 of which are protein-coding genes, four rRNA genes, 30 tRNA genes, and 18 duplicated genes in the inverted repeat region. The phylogenetic analysis indicated A. sterilis closely clustered with the cultivated oat, A. sativa L.

The complete chloroplast genome sequences of little millet (Panicum sumatrense Roth ex Roem. and Schult.) (Poaceae).

Little millet, Panicum sumatrense Roth ex Roem. & Schult., is an important cultivated species under the tribe Paniceae, sub-family Panicoideae and family Poaceae. In this study, for the first time we sequenced the complete chloroplast (cp) genome of P. sumatrense to investigate their phylogenetic relationship in the family Poaceae. The complete cp genome sequence of P. sumatrense is 139,384 bp in length with 38.6% overall GC content and exhibits a typical quadripartite structure comprising one pair of inverted repeats (22,723 bp) separated by a small single-copy region (12,583 bp) and a large single-copy region (81,355 bp). The P. sumatrense cp genome encodes 125 unique genes, which include 91 protein-coding genes, 4 rRNA genes, 30 tRNA genes, and 20 genes were duplicated in the inverted repeat region. This newly determined cp genome (P. sumatrense) could be valuable information for the breeding programs of this cereal crops in the family Poaceae.

New Genetic Loci Associated with Preharvest Sprouting and Its Evaluation Based on the Model Equation in Rice.

Preharvest sprouting (PHS) in rice panicles is an important quantitative trait that causes both yield losses and the deterioration of grain quality under unpredictable moisture conditions at the ripening stage. However, the molecular mechanism underlying PHS has not yet been elucidated. Here, we explored the genetic loci associated with PHS in rice and formulated a model regression equation for rapid screening for use in breeding programs. After re-sequencing 21 representative accessions for PHS and performing enrichment analysis, we found that approximately 20,000 SNPs revealed distinct allelic distributions between PHS resistant and susceptible accessions. Of these, 39 candidate SNP loci were selected, including previously reported QTLs. We analyzed the genotypes of 144 rice accessions to determine the association between PHS and the 39 candidate SNP loci, 10 of which were identified as significantly affecting PHS based on allele type. Based on the allele types of the SNP loci, we constructed a regression equation for evaluating PHS, accounting for an R2 value of 0.401 in japonica rice. We validated this equation using additional accessions, which exhibited a significant R2 value of 0.430 between the predicted values and actual measurements. The newly detected SNP loci and the model equation could facilitate marker-assisted selection to predict PHS in rice germplasm and breeding lines.

The complete chloroplast genome of Capsicum frutescens (Solanaceae).

PREMISE OF THE STUDY: We report the complete sequence of the chloroplast genome of Capsicum frutescens (Solanaceae), a species of chili pepper. METHODS AND RESULTS: Using an Illumina platform, we sequenced the chloroplast genome of C. frutescens. The total length of the genome is 156,817 bp, and the overall GC content is 37.7%. A pair of 25,792-bp inverted repeats is separated by small (17,853 bp) and large (87,380 bp) single-copy regions. The C. frutescens chloroplast genome encodes 132 unique genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Of these, seven genes are duplicated in the inverted repeats and 12 genes contain one or two introns. Comparative analysis with the reference chloroplast genome revealed 125 simple sequence repeat motifs and 34 variants, mostly located in the noncoding regions. CONCLUSIONS: The complete chloroplast genome sequence of C. frutescens reported here is a valuable genetic resource for Capsicum species.