Genetic Diversity Study of African Rice (Oryza glaberrima) and its Wild Relatives using Microsatellites Markers

The Africa Rice Center Gene Bank hold about 2,500 accessions of Oryza glaberrima. To understand well the genetic diversity in O. glaberrima and its wild species, the use of molecular tools is prominent. The sample consisted of 217 accessions of O. glaberrima, 46 of O. barthii and 7 of O. sativa (checks) was genotyped with 21 polymorphic microsatellites markers. A total of 245 alleles were detected with average 11.67 alleles per locus. Number of alleles was ranged from 2 (RM124) to 20 (RM536). The polymorphic information content value was 0.49 while the heterozygosity was 0.091. The result showed that the sample can be clustered into four genotypic groups. Two groups among them were homogeneous. The first one consisted of O. barthii accessions with 82 alleles in total with average 3.90 alleles per locus. However, the second one consisted of only O. glaberrima accessions with 122 alleles with average 5.80 alleles per locus. O. glaberrima accessions were analyzed using model-based population structure. Results revealed two groups among O. glaberrima accessions. At the end, the identified core collection has 26 accessions consisted of 16 O. glaberrima and 10 O. barthii based on 21 microsatellites markers.

Keragaan Pertumbuhan dan Produksi Aksesi-Aksesi Kacang Tunggak Lokal Asal Maluku

Cowpea belongs to minor legumes that have a prospect for future improvement as a supplementary food source. This research aimed to describe the vegetative growth of local cowpea and obtain genotypes with the highest performances of yield components and yields. This research was conducted as a single factor experiment that tested 14 accessions of cowpea. The study used a Completely Randomized Block Design with three replications. The results showed that KTm‑1, KTm-5, KTm-9, KTm-10, KTm-16, and KTm-26 accessions showed a denser appearance characteristic as indicated by their higher branch number and leaf number. Whereas, KTm-12 and KTm-20 had a characteristic of compact canopy appearance with a relatively short plant, but also with greater branch number and leaf number than that of the KT 6 national variety that did not have a dense canopy performance. The performance of KTm-5 and KTm-19 local accessions showed superior appearance in some of the observed yield variables, i.e. total pod number, full pod number, pod weight per plant, seed number, total seed number, and seed weight per plant, compared to the other local accessions. These two former local accessions showed the potential for all yield variables as good as those of the KT6 superior variety. For the seed number per pod and the seed locus number per pod, all local accessions except KTm-1 and KTm-17 were as excellent and high as those of the KT6 superior variety. Keywords: cowpea, local accessions, performance, yield ABSTRAK Kacang tunggak merupakan kacang-kacangan minor yang mempunyai prospek pengembangan ke depan sebagai sumber makanan tambahan. Penelitian bertujuan mendiskripsikan keragaan pertumbuhan vegetatif kacang tunggak lokal dan mendapatkan aksesi kacang tunggak lokal dengan hasil maupun komponen hasil tertinggi. Penelitian ini merupakan percobaan faktor tunggal yaitu menguji 14 aksesi kacang tunggak. Penelitian menggunakan Rancangan Acak Lengkap Berblok dengan tiga ulangan. Hasil penelitian menunjukkan KTm-1, KTm-5, KTm-9, KTm-10, KTm-16 dan KTm-26 memiliki karakteristik penampilan lebih rimbun berdasarkan jumlah cabang dan jumlah daun banyak. Sedangkan KTm-12 dan KTm-20 memiliki karakteristik rimbun dengan ciri tanaman relatif pendek namun jumlah cabang dan jumlah daunnya banyak dibandingkan varietas Nasional KT 6 dengan penampakan yang tidak rimbun. Keragaan produksi aksesi lokal KTm-5 dan KTm-19 memiliki penampilan lebih unggul pada beberapa peubah produksi yang diamati, yaitu jumlah polong total, jumlah polong bernas, bobot polong per tanaman, jumlah biji, jumlah biji bernas, bobot biji per tanaman, dibandingkan aksesi-aksesi lokal yang lain. Dua aksesi lokal tersebut berpotensi pada semua peubah produksi yang sama baik dengan varietas unggul KT6. Pada peubah jumlah biji per polong dan jumlah lokus biji per polong semua aksesi lokal sama baik dan tinggi dengan varietas unggul KT6 kecuali aksesi lokal KTm-1 dan KTm-17. Kata kunci: aksesi lokal, kacang tunggak, keragaan, produksi

Real-time PCR for the detection of precise transgene copy number in durum wheat

Recent results obtained in various crops indicate that real-time PCR could be a powerful tool for the detection and characterization of transgene locus structures. The determination of transgenic locus number through real-time PCR overcomes the problems linked to phenotypic segregation analysis (i.e. lack of detectable expression even when the transgenes are present) and can analyse hundreds of samples in a day, making it an efficient method for estimating gene copy number. Despite these advantages, many authors speak of “estimating” copy number by real-time PCR, and this is because the detection of a precise number of transgene depends on how well real-time PCR performs.This study was conducted to determine transgene copy number in transgenic wheat lines and to investigate potential variability in sensitivity and resolution of real-time chemistry by TaqMan probes. We have applied real-time PCR to a set of four transgenic durum wheat lines previously obtained. A total of 24 experiments (three experiments for two genes in each transgenic line) were conducted and standard curves were obtained from serial dilutions of the plasmids containing the genes of interest. The correlation coefficients ranged from 0.95 to 0.97. By using TaqMan quantitative real-time PCR we were able to detect 1 to 41 copies of transgenes per haploid genome in the DNA of homozygous T4 transformants. Although a slight variability was observed among PCR experiments, in our study we found real-time PCR to be a fast, sensitive and reliable method for the detection of transgene copy number in durum wheat, and a useful adjunct to Southern blot and FISH analyses to detect the presence of transgenic DNA in plant material.

Genetic history of the population of Atlantic salmon, Salmo salar L., under restoration in the Connecticut River, USA

The Connecticut River lost its Atlantic salmon population as a result of human activity 200 years ago. Cultured stocks, derived mainly from the Penobscot River, were employed to restore the population, and an annual run of salmon has been successfully re-established, although the population is not yet self-sustaining. We examined variation at microsatellite loci in historical scale and modern tissue samples to evaluate the degree and direction of any genetic changes that have occurred in the introduced population. The current genetic pattern of the Connecticut River population is very similar to that of its Penobscot River donor population. We found no differences in heterozygosity, mean number of alleles per locus, number of migrants, or FST values between the two populations, suggesting that no genetic bottlenecks had occurred during the restoration programme.

Variation in rDNA locus number and position among legume species and detection of 2 linked rDNA loci in the model Medicago truncatula by FISH

Within Fabaceae, legume species have a variable genome size, chromosome number, and ploidy level. The genome distribution of ribosomal genes, easily detectable by fluorescent in situ hybridization (FISH), is a good tool for anchoring physical and genetic comparative maps. The organisation of 45S rDNA and 5S loci was analysed by FISH in the 4 closely related species: Pisum sativum, Medicago truncatula, Medicago sativa (2 diploid taxa), and Lathyrus sativus. The 2 types of rDNA arrays displayed interspecific variation in locus number and location, but little intraspecific variation was detected. In the model legume, M. truncatula, the presence of 2 adjacent 45S rDNA loci was demonstrated, and the location of the rDNA loci was independent of the general evolution of the genome DNA. The different parameters relative to clustering of the rDNA loci in specific chromosome regions and the possible basis of rDNA instability are discussed.Key words: ribosomal genes, FISH, Medicago species, Pisum sativum, Lathyrus sativus, rDNA mobility.

Estimation of additive, dominance and epistatic variance components using finite locus models implemented with a single-site Gibbs and a descent graph sampler

In a previous contribution, we implemented a finite locus model (FLM) for estimating additive and dominance genetic variances via a Bayesian method and a single-site Gibbs sampler. We observed a dependency of dominance variance estimates on locus number in the analysis FLM. Here, we extended the FLM to include two-locus epistasis, and implemented the analysis with two genotype samplers (Gibbs and descent graph) and three different priors for genetic effects (uniform and variable across loci, uniform and constant across loci, and normal). Phenotypic data were simulated for two pedigrees with 6300 and 12300 individuals in closed populations, using several different, non-additive genetic models. Replications of these data were analysed with FLMs differing in the number of loci. Simulation results indicate that the dependency of non-additive genetic variance estimates on locus number persisted in all implementation strategies we investigated. However, this dependency was considerably diminished with normal priors for genetic effects as compared with uniform priors (constant or variable across loci). Descent graph sampling of genotypes modestly improved variance components estimation compared with Gibbs sampling. Moreover, a larger pedigree produced considerably better variance components estimation, suggesting this dependency might originate from data insufficiency. As the FLM represents an appealing alternative to the infinitesimal model for genetic parameter estimation and for inclusion of polygenic background variation in QTL mapping analyses, further improvements are warranted and might be achieved via improvement of the sampler or treatment of the number of loci as an unknown.