Polymorphic SSR Markers Research Articles

SSR and 18S rDNA based molecular profiling of Neopyropia yezoensis (Rhodophyta) in China: insight into genetic impact of laver aquaculture on wild resource

Neopyropia yezoensis is a typical intertidal seaweed and an indispensable species for conservation of seaweed resources. As one of the most important marine vegetables, the cultivation area of N. yezoensis has been largely increasing in the past decade and ranked the second highest among all the farmed seaweeds in China. It remains unknown whether large-scale cultivation of N. yezoensis has a genetic impact on wild populations. In this study, SSR markers and 18S rDNA were applied for diversity and genetic structure analysis of 22 N. yezoensis populations from North China. Twenty-two haplotypes were generated from 352 18S rDNA sequences and only three haplotypes were shared by both cultivated and wild populations. Based on 11 polymorphic SSR markers developed, the average polymorphism of the cultivated N. yezoensis populations was higher than that of the wild populations, with the percentage of polymorphic loci being 90.91% in most cultivated populations. The cultivated populations were clustered separately from the wild ones based on the population phylogenetic tree. This indicates that cultivated N. yezoensis populations are diverse and divergent from wild populations in China. However, there were cultivated individuals mixed with the wild ones based on the individual phylogenetic tree and STRUCTURE analysis. The genetic differentiation between cultivated and wild populations decreased with increasing cultivation time, suggesting a possible long-term and slow process of genetic introgression between cultivated N. yezoensis and the wild resource. The wild populations were grouped into two distinct clades by SSRs, with one distributed around the intersection between the Yellow Sea and the Bohai Sea, where the populations were characterized by a specific 18S rDNA haplotype. These findings provide useful insights into germplasm conservation, genetic breeding and improvement of N. yezoensis farming practices.

High-density genetic mapping of Fusarium head blight resistance and agronomic traits in spring wheat.

Fusarium head blight (FHB) has rapidly become a major challenge to successful wheat production and competitive end-use quality in western Canada. Continuous effort is required to develop germplasm with improved FHB resistance and understand how to incorporate the material into crossing schemes for marker-assisted selection and genomic selection. The aim of this study was to map quantitative trait loci (QTL) responsible for the expression of FHB resistance in two adapted cultivars and to evaluate their co-localization with plant height, days to maturity, days to heading, and awnedness. A large doubled haploid population of 775 lines developed from cultivars Carberry and AC Cadillac was assessed for FHB incidence and severity in nurseries near Portage la Prairie, Brandon, and Morden in different years, and for plant height, awnedness, days to heading, and days to maturity near Swift Current. An initial linkage map using a subset of 261 lines was constructed using 634 polymorphic DArT and SSR markers. QTL analysis revealed five resistance QTL on chromosomes 2A, 3B (two loci), 4B, and 5A. A second genetic map with increased marker density was constructed using the Infinium iSelect 90k SNP wheat array in addition to the previous DArT and SSR markers, which revealed two additional QTL on 6A and 6D. The complete population was genotyped, and a total of 6,806 Infinium iSelect 90k SNP polymorphic markers were used to identify 17 putative resistance QTL on 14 different chromosomes. As with the smaller population size and fewer markers, large-effect QTL were detected on 3B, 4B, and 5A that were consistently expressed across environments. FHB resistance QTL were co-localized with plant height QTL on chromosomes 4B, 6D, and 7D; days to heading on 2B, 3A, 4A, 4B, and 5A; and maturity on 3A, 4B, and 7D. A major QTL for awnedness was identified as being associated with FHB resistance on chromosome 5A. Nine small-effect QTL were not associated with any of the agronomic traits, whereas 13 QTL that were associated with agronomic traits did not co-localize with any of the FHB traits. There is an opportunity to select for improved FHB resistance within adapted cultivars by using markers associated with complementary QTL.

Genetic Diversity Assessment of Spanish and Some Endangered Tunisian Pea (Pisum sativum L.) Accessions Based on Microsatellite Markers (SSRs).

In the current investigation, 28 accessions of Spanish and Tunisian peas were characterized by eight SSR polymorphic markers to assess their genetic diversity. Many methods have been applied to evaluate these relationships including diversity indices, analysis of molecular variance, cluster analysis, and population structure. The means of diversity indices, the polymorphism information content (PIC), the allelic richness, and the Shannon information index were 0.51, 3.87, and 0.9, respectively. These results revealed a large polymorphism (84.15 %) which produced a higher degree of genetic distance amongst the accessions. The unweighted pair group approach with arithmetic mean divided the collection of these accessions into three major genetic clusters. Therefore, this article has clearly demonstrated the usefulness of the SSR markers that can significantly contribute to the management and conservation of pea germplasm in these countries, as well as to future reproduction.

Genetic Diversity and Population Structure Analysis to Construct a Core Collection from Safflower (Carthamus tinctorius L.) Germplasm through SSR Markers

Genetic resources are the fundamental source of diversity available to plant breeders for the improvement of desired traits. However, a large germplasm set is difficult to preserve and use as a working collection in genetic studies. Hence, the present study evaluates the genetic diversity of 3115 safflower accessions from the Indian National Gene Bank, including Indian cultivars, to develop a manageable set of accessions, with similar genetic variations of germplasm studied. A total of 18 polymorphic SSR markers were used. The genetic diversity analysis revealed that germplasm accessions were highly diverse and there is no correlation between genetic diversity and the geographical collection of germplasm or sourcing of germplasm. A core set was developed using a core hunter software with different levels of composition, and it was found that 10% of the accessions showed maximum gene diversity and represented an equal number of alleles and major allele frequency in the germplasm studied. The developed core consisted of 351 accessions, including Indian cultivars, and they were validated with various genetic parameters to ascertain that they were a true core set for the studied accessions of safflower germplasm.

Assessment of ethnobotanical uses, household, and regional genetic diversity of aroid species grown in northeastern India.

Aroids are an important group of indigenous tuber crops, grown widely for their leaves, petioles, stolons, corms, and cormels. A total of 53 genotypes were evaluated for their genetic diversity in northeastern region of India. At household level, a total of 16 landraces of Aroids were recorded having different ethnobotanical uses. Based on the population study under Jhum/Shifting farming, landrace Rengama was dominant in area with 47% of the total population followed by Tamachongkham and Tasakrek. However, Pugarkusu and Chigi occupied 33.0 and 24.0% of the population, respectively under backyard farming, and were considered as major landraces. Tamachongkham, high in acridity and total oxalate content (0.82%), was used for cooking with meat, while Tasakrek was used as a baby food due to high total sugar (>3.0%), low in acridity, and total oxalate content (<0.12%). The Simpson's diversity index of the backyards was higher (0.80) as compared to Jhum field (0.63). The genotypes showed wider variability in growth and yield attributes like; plant height (89.4-206.1 cm), number of side shoots (1.84-5.92), corm weight (38.0-683.3 g), cormel weight (14.0-348.3 g), yield (0.24-1.83 kg plant-1). Similarly, wide variations were also observed for quality traits like total sugar (1.93-4.94%); starch (15.32-32.49%), total oxalate (0.10-0.82%), and dry matter (16.75-27.08%) content. Except for total oxalate, all the growth and yield attributes have shown high heritability and moderate to high genetic advance. Molecular analysis (33 polymorphic SSR markers) detected a total of 136 alleles, ranged 3 to 8 alleles per marker. The observed heterozygosity (0.24) was less than expected heterozygosity (0.69). The group-wise maximum genetic divergence was observed between Colocasia fallax (cv. Chigi) to C. esculenta var. aquatilis (cv. Tharsing); C. fallax (cv. Chigi) to C. gigantea (cv. Ganima) and C. gigantea (cv. Ganima) to Xanthosoma spp., while it was least between eddo and dasheen. The findings indicated, a wider diversity and distinct ethnobotanical uses of Aroid landraces at the house hold levels, which should be conserved and popularized to ensure nutritional security.

Production and verification of lemon × acid lime hybrid populations via embryo rescue

Interspecific hybridization between canker-tolerant Konkan Seedless lemon (C. limon Burm) andcommercially grown Kagzi lime (C. aurantifolia Swingle) is significantly impeded by the occurrence of nucellarembryony. Hence, the objective of our work was to enhance hybrid seedlings’ recovery and to confirm theirhybridity through polymorphic SSR markers. Results revealed quite a satisfactory germination (&lt; 58%) from allthe stages of embryos and media used, but younger and oldest embryos produced more than 87% germinationon all three media tested. MS medium supplemented with 500 mg l-1 malt extract plus 1.5 mg l-1 GA3 and 20μll-1NAA proved better for the survival of plantlets, obtained from the culture of either aged or younger embryos,though it was highest in plantlets, obtained from the culture of 80-90 days old embryos. The seedlings obtainedfrom culture 80-90 old embryos (DAP or days after pollination) on MS medium supplemented with 500 mg l-1malt extract plus 1.5 mg l-1 GA3 and 20μl l-1 NAA had the highest root and shoot length at 30 days after culture(DAC). SSR loci CCSM4 and CAC-33 expressed the highest polymorphism, showing their ability to distinguishthe hybrids of Konkan Seedless (lemon) × Kagzi lime (acid lime) .

Comprehensive analysis of the laccase gene family in tea plant highlights its roles in development and stress responses

BackgroundLaccase (LAC) is the pivotal enzyme responsible for the polymerization of monolignols and stress responses in plants. However, the roles of LAC genes in plant development and tolerance to diverse stresses are still largely unknown, especially in tea plant (Camellia sinensis), one of the most economically important crops worldwide.ResultsIn total, 51 CsLAC genes were identified, they were unevenly distributed on different chromosomes and classified into six groups based on phylogenetic analysis. The CsLAC gene family had diverse intron–exon patterns and a highly conserved motif distribution. Cis-acting elements in the promoter demonstrated that promoter regions of CsLACs encode various elements associated with light, phytohormones, development and stresses. Collinearity analysis identified some orthologous gene pairs in C. sinensis and many paralogous gene pairs among C. sinensis, Arabidopsis and Populus. Tissue-specific expression profiles revealed that the majority of CsLACs had high expression in roots and stems and some members had specific expression patterns in other tissues, and the expression patterns of six genes by qRT‒PCR were highly consistent with the transcriptome data. Most CsLACs showed significant variation in their expression level under abiotic (cold and drought) and biotic (insect and fungus) stresses via transcriptome data. Among them, CsLAC3 was localized in the plasma membrane and its expression level increased significantly at 13 d under gray blight treatment. We found that 12 CsLACs were predicted to be targets of cs-miR397a, and most CsLACs showed opposite expression patterns compared to cs-miR397a under gray blight infection. Additionally, 18 highly polymorphic SSR markers were developed, these markers can be widely used for diverse genetic studies of tea plants.ConclusionsThis study provides a comprehensive understanding of the classification, evolution, structure, tissue-specific profiles, and (a)biotic stress responses of CsLAC genes. It also provides valuable genetic resources for functional characterization towards enhancing tea plant tolerance to multiple (a)biotic stresses.

Morphological and microsatellite marker-based characterization and diversity analysis of novel vegetable soybean [Glycine max (L.) Merrill

Vegetable soybean seeds are among the most popular and nutrient-dense beans in the world due to their delicious flavor, high yield, superior nutritional value, and low trypsin content. There is significant potential for this crop that Indian farmers do not fully appreciate because of the limited germplasm range. Therefore, the current study aims to identify the diverse lines of vegetable soybean and explore the diversity produced by hybridizing grain and vegetable-type soybean varieties. Indian researchers have not yet published work describing and analysing novel vegetable soybean for microsatellite markers and morphological traits. Sixty polymorphic SSR markers and 19 morphological traits were used to evaluate the genetic diversity of 21 newly developed vegetable soybean genotypes. A total of 238 alleles, ranging from 2 to 8, were found, with a mean of 3.97 alleles per locus. The polymorphism information content varied from 0.05 to 0.85, with an average of 0.60. A variation of 0.25-0.58 with a mean of 0.43 was observed for Jaccard's dissimilarity coefficient. The diverse genotypes identified can be helpful to understand the genetics of vegetable soybean traits and can be used in improvement programs; study also explains the utility of SSR markers for diversity analysis of vegetable soybean. Here, we identified the highly informative SSRs with PIC > 0.80 (satt199, satt165, satt167, satt191, satt183, satt202, and satt126), which apply to genetic structure analysis, mapping strategies, polymorphic marker surveys, and background selection in genomics-assisted breeding.

A Set of Highly Polymorphic Microsatellite Markers for Genetic Diversity Studies in the Genus Origanum

This study reports the development of a set of 20 highly polymorphic genomic SSR markers which can be used for both cultivar identification and genetic diversity studies in several Origanum species, including some of the most popular ones like Greek oregano (Origanum vulgare L. ssp. hirtum), common oregano (O. vulgare L. ssp. vulgare), and sweet marjoram (O. majorana L.). Analysis of the polymorphic information content (PIC) showed an average PIC value of 0.75 with a minimum of 0.41 and a maximum of 0.89, where 17 of the markers showed PIC values above 0.73. Comparative analysis of the genetic diversity of eight natural populations of Greek oregano in Bulgaria showed that six of the genomic SSR markers revealed significantly higher portions of genetic diversity in the populations, compared to 12 EST SSR markers used in our previous study. We also compared the performance of the same six genomic SSR markers with the results for eight SRAP primer combinations, which showed that SRAP markers captured more precisely the genetic structure in natural populations. The developed highly polymorphic genomic SSR markers can be successfully applied to evaluation of the genetic diversity in the genus Origanum, based on the expected and observed heterozygosity in the populations as well as for easy identification of breeding lines and cultivars based on unique SSR fingerprints.

First Report on Development of Genome-Wide Microsatellite Markers for Stock (Matthiola incana L.)

Stock (Matthiola incana (L.) R. Br.) is a famous annual ornamental plant with important ornamental and economic value. The lack of DNA molecular markers has limited genetic analysis, genome evolution, and marker-assisted selective breeding studies of M. incana. Therefore, more DNA markers are needed to support the further elucidation of the biology and genetics of M. incana. In this study, a high-quality genome of M. incana was initially assembled and a set of effective SSR primers was developed at the whole-genome level using genome data. A total of 45,612 loci of SSRs were identified; the di-nucleotide motifs were the most abundant (77.35%). In total, 43,540 primer pairs were designed, of which 300 were randomly selected for PCR validation, and as the success rate for amplification. In addition, 22 polymorphic SSR markers were used to analyze the genetic diversity of 40 stock varieties. Clustering analysis showed that all varieties could be divided into two clusters with a genetic distance of 0.68, which were highly consistent with their flower shape (potted or cut type). Moreover, we have verified that these SSR markers are effective and transferable within the Brassicaceae family. In this study, potential SSR molecular markers were successfully developed for 40 M. incana varieties using whole genome analysis, providing an important genetic tool for theoretical and applied research on M. incana.

A comprehensive evaluation of genetic diversity in persimmon (Diospyros kaki Thunb.) germplasms based on large-scale morphological traits and SSR markers

Persimmon (Diospyros kaki Thunb.) is an economically important fruit crop that originates from China, and has been cultivated for thousands of years. However, the genetic variation remains largely unknown. Evaluation of agronomic traits and genetic diversity in different persimmon germplasm plays an essential role in understanding of the persimmon breeding application and efficient resource utilization. Herein, we carried out the comprehensive evaluation of genetic diversity of persimmon germplasm based on large-scale morphological traits, and SSR markers. A total of 242 accessions were evaluated using 66 phenotypic characteristics and 12 highly polymorphic SSR markers. The results showed that 28 out of 66 descriptive characteristics presented coefficient of variation (CV) greater than 40%, indicating the different accessions of persimmon had rich genetic diversity. Furthermore, it showed varying degrees of correlation among 66 morphological traits. Correlation coefficient analysis present that growth potential was significantly correlated with flower sex, stigma length, grooves on fruit side, and sepal curl pose characters. In addition, we extracted seven components with justifying 85.17% of total variance based on principal component analysis (PCA), and fruit-related traits were the most important variables in distinguishing accessions. Combined cluster analysis based on morphological traits and SSR markers, we identified the four accessions of bud sport, 48 persimmon of synonyms, and two varieties of offspring. This study sheds light on genetic variation of persimmon based on morphological and SSR markers, and provides a valuable resource for marker-assisted breeding of this important fruit crop.

Temporal and Spatial Variation in the Population Structure of Spanish Fusarium circinatum Infecting Pine Stands

Fusarium circinatum is an introduced fungal pathogen extended to the northern regions of Spain that causes Pine Pitch Canker (PPC) disease. In this work, we analyzed the pathogen's genetic diversity to study changes over time and space since the first outbreak occurred in Spain. Using six polymorphic SSR markers, 15 MLGs were identified in 66 isolates, and only three haplotypes were found with frequencies higher than one. In general, genotypic diversity was low and decreased shortly over time in the northwestern regions while maintained at País Vasco, where only one haplotype (MLG32) was detected 10 years. This population also included isolates of a single mating type (MAT-2) and VCGs identified in only two groups, while isolates from NW regions were of both mating types and VCGs represented in 11 groups. The existence of haplotype MLG32 maintained on time and widely distributed suggests its good adaptation to the environment and the host. Results showed that the pathogen in País Vasco remains clearly differentiated from other northwestern populations. This fact was supported with no evidence of migration among regions. Results are explained by the asexual reproduction, but also selfing at least to a lesser extent that leads to identification of two new haplotypes.

Adaptation and High Yield Performance of Honglian Type Hybrid Rice in Pakistan with Desirable Agricultural Traits

Honglian type cytoplasmic male sterility (CMS) is one of the three known major CMS types of rice (Oryza sativa L.) commercially used in hybrid rice seed production. Hybrid rice generated by the Honglian type CMS is a special group of hybrid rice, having distinct agricultural characteristics. The main objective of the study was to screen out the Honglian hybrid rice adapted for growing in Pakistan based on desirable traits. Different Honglian-type hybrid rice varietieswere tested locally in different locations in Pakistan based on various desirabletraits. Three Honglian types of hybrids (HP1, HP2, HP3) performed well, had better agricultural traits and showed high yield potential over the check variety. Different qualitative and quantitative traits were studied to conclude the advantages of these varieties for Pakistani local adaptation evaluations. Forty-eight SSR markers were used to study the genetic diversities of the hybrids. Nine selected polymorphic SSR markers (RM-219, RM-236, RM-274, RM-253, RM-424, RM-567, RM-258, RM-481, RM-493) showed genetic variations among Honglian hybrid rice varieties through PCR analysis. In 2019 and 2020, the increment of the yield potential of HP1, HP2 and HP3 was better (+43.90%, +35.44%, +37.13% and +30.91%, +33.37%, +33.62%, respectively, in both years)than the check variety KSK-133. All the desirable traits were analyzed through Principal Component Analysis (PCA). The principal components with more than one eigenvalue showed more variability. The average variability of 74.78% was observed among genotypes and their desirable traits in both years. National Uniform Yield Trial (NUYT) and Distinctness, Uniformity, Stability (DUS) trials are being conducted under the supervision of National Coordinated Rice (NCR) and Federal Seed Certification and Registration Department (FSCRD), Government of Pakistan. In the 2020 trial, the average yield of 104 rice varieties/hybrids was 8608 kg/ha; HP1, HP2 and HP3 (8709 kg/ha, 8833 kg/ha, and 9338 kg/ha, respectively) were all higher than the average yield, and HP3 yield was higher than over check varieties (D-121, Guard-53). In the 2021 trial, the average yield of 137 varieties was 7616 kg/ha; the HP1 yield (7863 kg/ha) was higher than the average overcheck varieties/hybrids. Various qualitative and quantitative traits showed desirable genetic diversity among the rice hybrids. It was also observed that, under higher temperatures, the seeds setting rate of Honglian-type hybrid rice was stable, which is the guarantee for stable yield and rice production in Pakistan. Moreover, it was considerably better, suggesting that Honglian-type hybrid rice varieties can be grown in Pakistan because they are less risky under climate change, especially the global warming challenges.

Introgression of Drought Tolerance into Elite Basmati Rice Variety through Marker-Assisted Backcrossing

Drought is one of the major abiotic threat to rice production in the context of climate change. Super Basmati is an elite, fine grain basmati rice variety grown in Punjab, Pakistan. Due to drought sensitive in nature, its yield has been facing an alarming situation in production because of gradual decrease in irrigated water for a couple of years. Three reported novel QTLs for drought tolerance were selected for incorporation into Super Basmati by employing marker assisted selection strategy. IR55419-04 with novel QTLs was used as a donor parent. Foreground selection was performed by applying PCR based QTL linked SSR markers followed by recombinant selection by using 2–4 flanking markers. Background selection was exercised by using polymorphic SSR markers for maximum genome recovery of the Super Basmati. The individuals homozygous at the target QTLs and with maximum background of Super Basmati at the rest of the non-target genome was selected for evaluation of drought tolerance. Under drought stress conditions, the yields of all introgressed lines (ILs) were 44.2%–125.7% higher than recurrent parent. Six superior ILs that are drought tolerant and very similar to Super Basmati in terms of agronomic and grain quality traits are marked for release as drought-tolerant varieties in arid regions or for use in breeding programs of high grain quality and drought-tolerant parents.

Development of Polymorphic SSR Markers in Chinese Water Chestnut Based on RAD-seq

Development of Polymorphic SSR Markers in Chinese Water Chestnut Based on RAD-seq

Genetic analysis and identification of QTLs associated with yield-enhancing traits in Oryza sativa IR64 × Oryza glaberrima interspecific backcross populations

Context Broadening the gene pool of staple food crops by incorporating desirable genes from wild/relative species is way to achieve higher genetic gains. The African rice species Oryza glaberrima Steud. is a source of genes for genetic improvement of Oryza sativa L. to various biotic and abiotic stresses. Aim The study was undertaken to identify genomic regions associated with yield and yield-related traits in interspecific backcross mapping populations derived from variety IR64 (O. sativa indica) × O. glaberrima. Methods The BC1F2 and BC1F2:3 populations were phenotyped for days to 50% flowering, plant height, number of tillers, number of productive tillers, panicle length, spikelet fertility and grain yield under irrigated conditions. The BC1F2 population was genotyped with 99 genome-wide polymorphic SSR markers. Quantitative trait loci (QTLs) associated with yield-enhancing traits were identified through single marker analysis. Key results Significant genetic variability was observed with moderate to high heritability in mapping populations. Genotyping revealed the presence of segregation distortion and skewed genome composition. Single marker analysis identified 20 QTLs linked to the studied traits. A QTL linked to grain yield, qGY-4.1, derived from O. glaberrima was found in both populations with high phenotypic variance. The chromosome region around marker RM510 was identified as a QTL hotspot and putative candidate genes were identified. Conclusions Our study demonstrates that O. glaberrima can serve as a valuable genetic resource for genetic improvement of yield-enhancing traits in O. sativa cultivars. Implications The identified QTLs regions can be employed in molecular breeding. The promising introgression lines identified can be used as pre-breeding lines in future breeding programs.

Horticultural, chemical and genetic diversity using SSR markers in Leek germplasm collection

A total of twenty-three leek accessions, obtained from the German genebank in Gatersleben and the United States Department of Agriculture genebank, in addition to local genotype were phenotyped and genotyped to study the phenotypic and genetic diversity as well as population structure. Significant and broad variation was found among the accessions in terms of morphological (plant height and total yield), minerals content (nitrogen, phosphorus and sulfur) and bio-chemical (carbohydrates, phenols, thiosulfanates and allicin) traits. Our results identified promising accessions (Kong Richard, G-1722 and Kumanovski) for cultivation under Egyptian conditions, as they recorded the highest plant growth and yield. Also, a total of 152 alleles were obtained from 5 SSR polymorphic markers and high average number of alleles per locus (NA=30.4), heterozygosity per locus (Ho= 0.36) and polymorphism information content (PIC= 0.97) were reported, indicating that the used SSR primers were useful tool in detecting genetic variability among leek genotypes in the current leek collection. In addition, the genetic structure using multivariate, phylogenetic and model based methods generally and clearly separated these accessions into two different groups according to their life form (i.e., perennial vs. biennial genotypes). Moreover, Single Marker Analysis (SMA) identified candidate SSR markers associated with yield-related traits and allicin content. In conclusion, the results of the current research have provided important insights into the phenotypic and genetic diversity of leek's genebank accessions using morphological, minerals, bio-chemical content as well as SSR markers, for the first time, providing valuable information for researchers and breeders for future studies.

The resurrection of sweet corn inbred SC11-2 using marker aided breeding for β-carotene

Sweet corn has dominated the urban market due to its sweetness, tenderness, and ease of digestibility. It's import and export values have dramatically increased during the past 10 years as a fresh, processed, and preserved commodity. However, the commercially available sweet corns are deficient in β-carotene. In our study, we introgressed the favorable allele of crtRB1 (responsible for high β-carotene) into the recurrent sweet corn inbred SC11-2 from maize donor parent UMI1230β1+ to develop the β-carotene-rich sweet corn genotype by marker aided breeding. The crtRB1 3′TE InDel marker was utilized for foreground selection of favorable genotype. A total of 103 polymorphic SSR markers were employed for background selection, resulting in a 96% recovery of recurrent parent genome (RPG). We recorded high β-carotene content (9.878–10.645 μg/g) in the introgressed lines compared to the recurrent parent, SC11-2 (0.989 μg/g). The sugar content ranged from 18 to 19.10% and was on par with the recurrent parent (20.40%). These biofortified inbreds can be used as a donor in maize breeding programs to develop sweet corn genotypes with high β-carotene content.

Microsatellite analysis and polymorphic marker development based on the full-length transcriptome of Camellia chekiangoleosa

Camellia chekiangoleosa is a popular variety of Oil-camellia that has high oil production and ornamental value. Microsatellite (SSR) markers are the preferred tool for the molecular marker-assisted breeding of C. chekiangoleosa. By focusing on the problems of the low development efficiency of polymorphic SSR markers and the lack of available functional markers in Oil-camellia, we identified 97,510 SSR loci based on the full-length transcriptome sequence of C. chekiangoleosa. An analysis of SSR characteristics showed that mononucleotide (51.29%) and dinucleotide (34.36%) SSRs were the main repeat types. The main SSR distribution areas based on proportion covered were ordered as follows: 5'UTR > 3'UTR > CDS. By comparing our data with those in databases such as GO and KEGG, we obtained functional annotations of unigene sequences containing SSR sites. The data showed that the amplification efficiency of the SSR primers was 51.72%, and the development efficiency of polymorphic SSR primers was 26.72%. Experiments verified that dinucleotide and pentanucleotide SSRs located in UTR regions could produce more polymorphic markers. An investigation into the genetic diversity of several C. chekiangoleosa populations also suggested that the developed SSR markers had higher levels of polymorphism. This study will provide a reference and high-quality markers for the large-scale development of functional SSR markers and genetic research in Oil-camellia.

Development and Application of Polymorphic SSR Markers in Luffa cylindrica

Development and Application of Polymorphic SSR Markers in Luffa cylindrica