Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

Genetic diversity and population structure of Luffa acutangula accessions in a Thailand collection using SNP markers

This study explored a germplasm consisting of 112 Luffa acutangula (ridge gourd) accessions mainly from Thailand, and some accessions from Vietnam, China, Philippines, Indonesia, USA, Bangladesh and Laos for an analysis of the population structure and underlying genetic diversity using 2,834 SNPs. STRUCTURE analysis (ΔK at K=6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. The phylogenetic tree showed the diversity of L. acutangula in Thailand, and accessions from other countries apart from Thailand were grouped together in the same branches. In STRUCTURE, subpopulation 2 contained only accessions from Thailand while other subpopulations contained a combination of accessions from Thailand and from other countries. When plotted, the STRUCTURE bars to the area of collection, it revealed the geneflow from the surrounding places nearby as indicated by the admixed genetic in the STRUCTURE bars. AMOVA based on STRUCTURE clustering showed the variation between populations (12.83%) and confirmed the absence of population structure in subpopulations (−10.59%). There was a distinguishing characteristic fruit shape and length in each subpopulation. The ample genetic diversity found in the L. acutangula germplasm can be utilized in ridge gourd breeding programs to help meet the demands and needs of both consumers and farmers.

Population structure and phylogenetic analysis of laboratory rabbits in Taiwan based on microsatellite markers

Laboratory rabbits used in Taiwan are primarily supplied by the Livestock Research Institute (LRI) and the Animal Drugs Inspection Branch (ADIB) of the Animal Health Research Institute. An analysis of the genetic characteristics and structure of these populations would thus be a fundamental step in building a long-term management programme for maintaining stable animal quality and preserving the genetic variation among the populations. In this study, DNA samples were isolated from founders of 5 populations: New Zealand White rabbits (NZW) and Japanese White rabbits (JPN) from the ADIB, NZW and Rex rabbits (REX) from the LRI, and NZW from a private rabbit breeding farm in Ban Ciao (BC). A set of microsatellite markers, 18 in total, was designed for genetic analysis. The average values for the allele number (Na), effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (H_E), and Wright’s fixation index (F_IS) were 5.50, 2.437, 0.442, 0.568 and 0.232, respectively. These results revealed that this set of microsatellite markers has high diversity and that the major local populations have a tendency toward inbreeding. At the same time, analysis of molecular variance results showed that the laboratory rabbits used in Taiwan have maintained a high level of within-population genetic differentiation (83%). The genetic differentiation among clusters was moderate (F_ST=0.18), and Bayesian cluster analysis showed that the most likely number of groups was 4 (K=4). Principal component analysis (PCA) also showed 4 divergent clusters. The LRI and BC NZW populations were not separated when K=4 was used in a Structure software analysis and were also hard to split until principal component 3 in PCA. The individual unrooted phylogenetic tree showed that the 5 populations were separated, except that some individuals from the LRI NZW population overlapped with the ADIB NZW and BC NZW populations. As such, in order to counteract the reduced F_IS (0.232) and maximise heterozygosity, the 3 NZW populations could be interbred or have new genes introduced into them. The set of microsatellite markers used herein was useful for studying the relationships and genetic diversities among these rabbit populations of Taiwan. Based on the resulting data, rabbit farms in Taiwan could select parental stocks for planned mating in the future as part of strategies to preserve and restore the rational breeding of laboratory rabbits.

Identification and genes expression analysis of ATP-dependent phosphofructokinase family members among three Saccharum species

Sugarcane contributes ~80% of sugar production in the world and is an established biofuel crop. In working towards understanding the molecular basis of high sucrose accumulation, we have annotated and analysed the ATP-dependent phosphofructokinase (PFK) gene family that catalyses the phosphorylation of D-fructose 6-phosphate to D-fructose 1,6-bisphosphate. PFKs play an essential role in sucrose metabolism in plants and their expression patterns are unknown in sugarcane. In this study, based on the sorghum genome and sugarcane EST database, 10 PFK gene members were annotated and further verified by PCR using sugarcane genomic DNA. An unrooted phylogenetic tree was constructed with the deduced protein sequences of PFKs that were from the assembly of cDNA library of sugarcane and other plants. The results showed that gene duplication events and the retention rate after genome wide or segmental duplications occurred in higher frequency in monocots than in dicots and the genes in subgroup II of group III were likely originated from recent duplication events. Quantitative RT–PCR was performed to investigate the gene expression of 10 PFK genes in five tissues of three Saccharum species, including two developmental stages in leaves and three in culms. Of the PFK family members in sugarcane, ScPFK6, 7 and 8 appeared to be the primary isoforms based on the highly abundant expression of these three genes. ScPFK7 showed high expression level in the leaves, suggesting a potential role in sucrose metabolism. ScPFK8 had lower expression level in Saccharum officinarum L. than in the other two species, suggesting negative regulation of sucrose metabolism, which might have contributed to the high sugar content of S. officinarum. The genes in monocot specific subgroup II of group III, PFK7, 8 and 9, showed variation among the three Saccharum species, suggesting potential functional redundancy. Our results provide detailed annotation and analysis of the PFK gene family in sugarcane. Further elucidation of the role of ScPFK8 in the domestication process of sugarcane would be useful.

A Phylogeny of Bacterial RNA Nucleotidyltransferases: Bacillus halodurans Contains Two tRNA Nucleotidyltransferases

ABSTRACT We have analyzed the distribution of RNA nucleotidyltransferases from the family that includes poly(A) polymerases (PAP) and tRNA nucleotidyltransferases (TNT) in 43 bacterial species. Genes of several bacterial species encode only one member of the nucleotidyltransferase superfamily (NTSF), and if that protein functions as a TNT, those organisms may not contain a poly(A) polymerase I like that of Escherichia coli. The genomes of several of the species examined encode more than one member of the nucleotidyltransferase superfamily. The function of some of those proteins is known, but in most cases no biochemical activity has been assigned to the NTSF. The NTSF protein sequences were used to construct an unrooted phylogenetic tree. To learn more about the function of the NTSFs in species whose genomes encode more than one, we have examined Bacillus halodurans. We have demonstrated that B. halodurans adds poly(A) tails to the 3′ ends of RNAs in vivo. We have shown that the genes for both of the NTSFs encoded by the B. halodurans genome are transcribed in vivo. We have cloned, overexpressed, and purified the two NTSFs and have shown that neither functions as poly(A) polymerase in vitro. Rather, the two proteins function as tRNA nucleotidyltransferases, and our data suggest that, like some of the deep branching bacterial species previously studied by others, B. halodurans possesses separate CC- and A-adding tRNA nucleotidyltransferases. These observations raise the interesting question of the identity of the enzyme responsible for RNA polyadenylation in Bacillus.

Sequence Analysis of the Chalcone Synthase Gene Intron in Four Petunia Jussieu Taxa

The sequence of the intron within the chalcone synthase A gene (ChsA) was used to characterize Petunia integrifolia subsp. integrifolia var. depauperata (Fries) Smith et Downs, P. altiplana Ando et Hashimoto, P. littoralis Smith et Downs, and an unknown taxon from the town of Torres in Brazil. Based upon the intron, the Torres taxon most closely resembled P. integrifolia. The unrooted phylogenetic tree suggested that P. integrifolia was more closely related to P. littoralis than P. altiplana.