Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing

Little millet is a climate-resilient and high-nutrient value plant. The lack of molecular markers severely limits the adoption of modern genomic approaches in millet breeding studies. Here the transcriptome of three samples were sequenced. A total of 4443 genic-SSR motifs were identified in 30,220 unigene sequences. SSRs were found at a rate of 12.25 percent, with an average of one SSR locus per 10 kb. Among different repeat motifs, tri-nucleotide repeat (66.67) was the most abundant one, followed by di- (27.39P), and tetra- (3.83P) repeats. CDS contained fewer motifs with the majority of tri-nucleotides, while 3′ and 5′ UTR carry more motifs but have shorter repeats. Functional annotation of unigenes containing microsatellites, revealed that most of them were linked to metabolism, gene expression regulation, and response to environmental stresses. Fifty primers were randomly chosen and validated in five little millet and 20 minor millet genotypes; 48% showed polymorphism, with a high transferability (70%) rate. Identified microsatellites can be a noteworthy resource for future research into QTL-based breeding, genetic resource conservation, MAS selection, and evolutionary genetics.

Analysis of genetic parameters of reproductive traits in conserved breed sows raised in Poland

The aim of the study was to estimate the genetic parameters for reproductive performance in native breeds sows covered by genetic resource conservation programmes in Poland. The study used data on reproductive performance of 1,182 Złotnicka White sows, 1,648 Złotnicka Spotted sows and 1,180 Puławska sows. The following traits were analysed: age at first farrowing, number of piglets born alive, number of piglets at 21 days of age and farrowing interval. Covariance components and genetic parameters were estimated using an REML animal model with different combinations of fixed and random effects. Convergence of the iterative process was achieved by the selection of the AIREML algorithm. The estimated values of the coefficients of heritability for the number of piglets born ranged from h2 = 0.09 in the Puławska breed to h2 = 0.30 in the Złotnicka White breed. For the number of piglets reared, they varied between h2 = 0.09 in the Złotnicka Spotted breed to h2 = 0.27 in the Puławska breed. The heritability values for age at first farrowing and farrowing interval were higher, and ranged from 0.4 to 0.5. The significant positive and negative coefficients of phenotypic correlation, estimated between age at first farrowing and farrowing interval with the number of piglets born alive and reared per litter, suggest that the native pig breeds should be bred in keeping with their breed predispositions.

Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers

Background: Vernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand for its natural epoxidized oil, which can be used for the manufacturing of oleochemicals such as paints, plastic formulations (polyvinyl chloride), and pharmaceutical products. Assessment of the extent of genetic diversity in V. galamensis was the first and the most step in cultivation, breeding and genetic resource conservation. Hence, this study was aimed to assess the genetic diversity and population structure of this plant from different agro-ecologies in Ethiopia using SSR markers. Results: Twenty SSR markers were used for genetic diversity analyses of 150 individual V. galamensis accessions representing 10 populations, from which a total of 79 bands were identified for the 20 loci. All the loci used showed high polymorphism that ranged from 0.50 to 0.96, while the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The molecular variance analysis (AMOVA) showed significant variations among populations which accounted for 11% of the variations. Populations clustering showed that the dendrogram and principal coordinate’s analysis roughly classified the accessions into four groups. However, the Bayesian model-based clustering (STRUCTURE) grouped into 6 (K = 6) major gene pools. Since, the cluster and the STRUCTURE analyses did not group the populations into sharply distinct clusters, due to presence of gene flow and mode of reproduction of the plant. Conclusions: The SSR molecular markers used in this study are highly polymorphic. Among the ten populations, East Showa and East Hararghe revealed higher genetic diversity, signaled that these areas are the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content, and population clusters are important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.

Genetic Diversity and Population Structure of Polish Konik Horse Based on Individuals from All the Male Founder Lines and Microsatellite Markers

The Polish Konik horse is a primitive native breed included in the genetic resource conservation program in Poland. After World War II, intensive breeding work began, aimed at rebuilding this breed. Now, the whole Polish Konik population is represented by six male founder lines (Wicek, Myszak, Glejt I, Goraj, Chochlik and Liliput). Individuals representing all six paternal lineages were selected based on their breeding documentation. We performed a fragment analysis with 17 microsatellite markers (STRs) recommended by the International Society for Animal Genetics (ISAG). The genetic diversity and structure within the paternal lineages and the whole of the studied group were investigated. The average allelic richness was 6.497 for the whole studied group. The fixation index (FST; measure of population differentiation) was low (about 3%), the mean inbreeding coefficient (FIT) was low and close to 0, and the mean inbreeding index value (FIS) was negative. The mean expected heterozygosity was established at 0.7046 and was lower than the observed heterozygosity. The power of discrimination and power of exclusion were 99.9999%. The cumulative parentage exclusion probability equaled 99.9269% when one parental genotype was known and 99.9996% with both parents’ genotypic information was available. About 3% of the genetic variation was caused by differences in the breed origin and about 97% was attributed to differences among individuals. Our analysis revealed that there has been no inbreeding in the Polish Konik breed for the studied population. The genetic diversity was high, and its parameters were similar to those calculated for native breeds from other countries reported in the literature. However, due to the small number of breed founders and paternal lineages with unknown representation, the population’s genetic diversity and structure should be monitored regularly.

Social Valuation of Genebank Activities: Assessing Public Demand for Genetic Resource Conservation in the Czech Republic

The use of diverse genetic resources to breed improved crop varieties has been a key driver of agricultural productivity improvements in the past century. At the same time, the adoption of modern varieties has contributed to substantial loss of traditional varieties. In this analysis, we estimate the social value provided by several proposed crop diversity conservation programs to be carried out by the Czech genebank system. We use a double-bounded dichotomous choice model to estimate the willingness-to-pay (WTP) for conserving additional crop varieties in the genebank for ten years using data collected through an online contingent valuation survey administered to a sample representative of the general Czech population (1037 respondents) and a smaller sub-sample representative of the agricultural region of South Moravia (500 respondents). Mean WTP was found to be about $9 for both the Czech and S. Moravian sub-samples, corresponding to country-wide benefits of ~$68 million. These benefits increase by 6–7% for every ten varieties conserved, implying total welfare benefits of ~$84 million for a program conserving the maximum number of 35 additional crop varieties offered in the experiment. The study illustrates an empirical approach of potential value for policymakers responsible for determining funding levels for genetic resource conservation.

Independent domestication events in the blue-cheese fungusPenicillium roqueforti

Domestication provides an excellent framework for studying adaptive divergence. Using population genomics and phenotypic assays, we reconstructed the domestication history of the blue cheese moldPenicillium roqueforti.We showed that this fungus was domesticated twice independently. The population used in Roquefort originated from an old domestication event associated with weak bottlenecks and exhibited traits beneficial for pre-industrial cheese production (slower growth in cheese and greater spore production on bread, the traditional multiplication medium). The other cheese population originated more recently from the selection of a single clonal lineage, was associated to all types of blue cheese worldwide but Roquefort, and displayed phenotypes more suited for industrial cheese production (high lipolytic activity, efficient cheese cavity colonization ability and salt tolerance). We detected genomic regions affected by recent positive selection and putative horizontal gene transfers. This study sheds light on the processes of rapid adaptation and raises questions about genetic resource conservation.