InDel Marker Development and QTL Analysis of Agronomic Traits in Mung Bean [Vigna Radiate (L.) Wilczek]

The stem color of young mung bean is a very useful tool in germplasm identification. Flowering time and plant height (PH) are known to be strongly correlated with crop adaption and yield. However, few studies have focused on elucidating the genetic mechanisms that regulate these five particular traits: young stem color (YSC), days to first flowering (DFF), days to maturity (DM), PH, and nodes on main stem (NMS). In this study, a genetic linkage map for the F2 population was constructed using 129 InDel markers that were developed based on the sequence variations between parents. A total of 14 QTLs related to YSC, DFF, DM, PH, and NMS were detected. These QTLs were distributed on six chromosomes (1, 3, 4, 6, 7, and 10), which individually accounted for 1.32% to 90.07% of the total phenotypic variation. Using a short and high-density linkage map for the F3 population, six of the seven QTLs which clustered at two intervals on chromosomes 3 and 10 were detected again. Further analysis found that four QTLs between InDel markers R3-15 and R3-19 controlled DFF, DM, PH, and NMS, and each QTL accounted for a large percent of the total phenotypic variation. Analysis of two F2:3 lines also found that the phenotype was highly corresponded to its genotype which is between R3-15 and R3-19. Phenotype and genotype analysis for 30 mung bean accessions showed that the major effect QTL qDFF3 was a key regulator for days to DFF. Using a map-based cloning method, the major effect QTL qYSC4 for YSC was mapped in a 347 Kb interval on chromosome 4. Candidate gene analysis showed that sequence variations and expression level differences existed in the predicted candidate gene between the parents. These results provide a theoretical basis for cloning these QTLs and marker-assisted selection.

Comparative Chloroplast Genome Analysis of Impatiens Species (Balsaminaceae) in the Karst Area of China: Insights Into Genome Evolution and Phylogenomic Implications.

Background: Impatiens, a controversial and complex genus, which belongs to the family Balsaminaceae with approximately 1000 species. The genus is well known for economical, medicinal, ornamental, and horticultural values. However, Due to the morphological features and insufficient genomic resources, their analyses of germplasm identification and molecular phylogeny are very limited. Results: We have sequenced the chloroplast genomes of six different species (I. chlorosepala, I. fanjingshanica, I. guizhouensis, I. linearisepala, I. loulanensis, and I. stenosepala) in the karst area of China and compared them with previously published species and the monospecific sister Hydrocera triflora belonging to Balsaminaceae family. We comtrasted the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships. The 12 complete chloroplast genomes of the Balsaminaceae species ranged in size from 151,538 bp (I. fanjingshanica) to 154,189bp (H. triflora ) encoded 114 total distinct genes except for I. glandulifera and H. triflora, including 81 protein-coding, 29 transfer RNA genes(tRNA), and 4 ribosomal RNA genes (rRNA). Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were found. Divergent hotspots regions psbK-psbI,trnT-GGU-psbD, rpl36-rps8, rpoB-trnC-GCA, trnK-UUU-rps16, trnQ-UUG, trnP-UGG-psaJ, trnT-UGU-trnL-UAA, and ycf4-cemA were identified in the 12 Balsaminaceae chloroplast genomes, which could be suitable for species identification and phylogenetic studies. Additionally, phylogenetic relationships based on Maximum likelihood (ML) and Bayesian inference (BI) among whole chloroplast genomes showed that H. triflora was the basal group in Balsaminaceae and I. guizhouensis was the basal group in impatiens species. Besides this, cultivated species(I. balsamina, I. hawkeri, and I. walleriana) were clustered together. Conclusion: Our study provides detailed information about nucleotide diversity hotspots and characterized types of repeats, which can be used for developing molecular markers applicable in Balsaminaceae species. And also we reconstructed and analyzed the relationships of some impatiens species and discovered their status based on the complete chloroplast genomes. The current study might provide valuable significant genomic information for the systematics and evolution in the Balsaminaceae.

Complete Chloroplast Genomes and Comparative Analyses of L. chinensis, L. anhuiensis, and L. aurea (Amaryllidaceae)

The genus Lycoris (about 20 species) includes important medicinal and ornamental plants. Due to the similar morphological features and insufficient genomic resources, germplasm identification and molecular phylogeny analysis are very limited. Here, we sequenced the complete chloroplast genomes of L. chinensis, L. anhuiensis, and L. aurea; they have very similar morphological traits that make it difficult to identify. The full length of their cp genomes was nearly 158k bp with the same guanine-cytosine content of 37.8%. A total of 137 genes were annotated, including 87 protein-coding genes, 42 tRNAs, and eight rRNAs. A comparative analysis revealed the conservation in sequence size, GC content, and gene content. Some variations were observed in repeat structures, gene expansion on the IR-SC (Inverted Repeat-Single-Copy) boundary regions. Together with the cpSSR (chloroplast simple sequence repeats), these genetic variations are useful to develop molecular markers for germplasm identification. Phylogenetic analysis showed that seven Lycoris species were clustered into a monophyletic group, and closed to Narcissus in Amaryllidaceae. L. chinensis, L. anhuiensis, and L. longituba were clustered together, suggesting that they were very likely to be derived from one species, and had the same ancestor with L. squamigera. Our results provided information on the study of genetic diversity, origins or relatedness of native species, and the identification of cultivars.

Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweetpotato [Ipomoea batatas L. (Lam) cv. Taizhong6]

Background: Sweetpotato is a multifunctional root crop with many essential nutrients and bioactive compounds. Due to its genetic complexity and lack of genomic resources, efficient genetic studies, and cultivar development lags far behind other major crops. Simple sequence repeats (SSRs) offer an effective molecular marker technology for molecular-based breeding and for locating important loci in crop plants, but only a few have previously been developed in sweetpotato. Results: To further explore new SSR markers and accelerate its use in sweetpotato genetic studies, genome-wide characterization and development of SSR markers were performed using the recently published genome of sweetpotato cultivar, Taizhong6. In this study, a set of 2,431 primer pairs were developed from 133,727 SSRs identified in the sweetpotato genome using the Perl script MISA software. The average frequency was one SSR per 6.26 kb with dinucleotides (38.5%) being the most dominant repeat motif. The main motif types in all repeats were AT/AT, AAT/ATT, A/T, AAAT/ATTT, AAAAT/ATTTT and AAAAAT/ATTTTT accounting for 78.29% of the total SSRs. 50% of the 100 randomly selected primer pairs amplified 251 alleles and the average number of alleles was 5.02 alleles per locus with a range of 1 to 13 alleles. The UPGMA cluster analysis grouped the 24 sweetpotato materials into four clusters at a similarity coefficient of 0.68. Conclusion: The SSR markers currently developed will provide valuable genetic resources for germplasm identification, genetic diversity analysis, and functional genomics studies in sweetpotato and related species.

Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweet potato [Ipomoea batatas L. (Lam) cv. Taizhong6]

The genetic complexity and the lack of genomic resources in sweet potato make genetic improvement extremely challenging. Simple sequence repeats (SSRs) offer an effective molecular marker technology for molecular-based breeding and for locating important loci in crop plants, but only a few have previously been developed in sweet potato. To explore new SSR markers and accelerate its use in sweet potato, we developed a set of 2,431 primer pairs from 133,727 SSRs identified in the sweet potato genome using the Perl script MISA software. The average frequency was one SSR per 6.26 kb with dinucleotides (38.5%) being the most dominant repeat motif. The main motif types in all repeats were AT/AT, AAT/ATT, A/T, AAAT/ATTT, AAAAT/ATTTT and AAAAAT/ATTTTT accounting for 78.29% of the total SSRs. Out of the 100 randomly selected primer pairs, 50% produced clear bands and amplified 251 alleles. On average, the number of alleles was 5.02 per locus for values ranging from 1 to 13 alleles. The UPGMA cluster analysis grouped the 24 sweet potato materials into four clusters at a similarity coefficient of 0.68 showing no relationship between the genotypes and the geographic sources of germplasm. The SSR markers currently developed will provide valuable genetic resources for germplasm identification, and accelerate studies on genetic diversity in sweet potato and related species.

GC-MS Analysis of Volatile Components in Partridge Tea (Mallotus obongifolius)

Partridge tea is one of the famous local herbal teas of Hainan Island, China. In the present study, headspace solid-phase microextraction and gas chromatography-mass spectrometry were combined to determine and analyze the volatile components in the red and green leaves of partridge tea. Seventeen volatile components were identified in the red young leaves. The olefins, alkanes, and alcohols accounted for 71.24%, 1.1%, and 0.54%, among which the main components were caryophyllene (22.50%), humulene (18.73%), and α-guaiene (8.78%), respectively. Twenty volatile components were identified from red mature leaves, including 34.74% olefins, 6.14% esters, and 3.11% acids. Eighteen volatile components were identified from green young leaves, among which olefins (70.52%), alkanes (4.32%), and alcohol (0.89%) were the major components. Nineteen volatile components were identified from green mature leaves, among which the olefins, esters, and acids were the major components with the contents of 46.04%, 6.38%, and 1.37%, respectively. Results showed that the major volatile components of partridge tea were olefins, in which caryophyllene was the most abundant. The contents of volatile components between red leaves and green leaves had notable differences, which might be useful for germplasm identification of partridge tea.