Harnessing diversity of Lactococcus lactis from raw goat milk: Design of an indigenous starter for the production of Rocamadour, a French PDO cheese

Twenty-four strains of Lactococcus lactis isolated from raw goat milk collected in the Rocamadour PDO area were analysed by MLST typing and phenotypic characterisation. The strains were combined to design an indigenous starter for the production of Rocamadour PDO cheese. The strains were divided into three classes based on their technological properties: acidifying and proteolytic strains in class I (12/24 strains), slightly acidifying and non-proteolytic strains in class II (2/24 strains), and non-acidifying and non-proteolytic strains in class III (10/24 strains). Interestingly, all but three strains (21/24) produced diacetyl/acetoin despite not having citrate metabolism genes, as would classically be expected for the production of these aroma compounds. Three strains (EIP07A, EIP13D, and EIP20B) were selected for the indigenous starter based on the following inclusion/exclusion criteria: (i) no negative interactions between included strains, (ii) ability to metabolize lactose and at least one strain with the prtP gene and/or capable of producing diacetyl/acetoin, and (iii) selected strains derived from different farms to maximise genetic and phenotypic diversity. Despite consisting exclusively of L. lactis strains, the designed indigenous starter allowed reproducible cheese production with performances similar to those obtained with an industrial starter and with the sensory qualities expected of Rocamadour PDO cheese.

Growth performance, phenotypic traits, and antioxidant responses of the rotifer Brachionus plicatilis under different proportions of Phaeocystis globosa

Harmful Phaeocystis blooms disrupt seawater recreation and pose serious challenges to aquatic animals. The growth performance, phenotypic traits, and antioxidant responses of Brachionus plicatilis Müller to different proportions of Phaeocystis globosa were evaluated. B. plicatilis rotifers were exposed to cultures with Chlorella sp. and P. globosa alone and in mixtures of these two algae with proportions of 25%, 50%, and 75%. The total proportions of the two algae were maintained at 100%. Results showed that P. globosa inhibited the rotifer net reproduction rate, intrinsic growth rate, and finite rate of increase (P < 0.01). It induced the formation of defense phenotypic traits in terms of the increased posterolateral spine length and the reduced body length, swimming speed, and grazing rate of B. plicatilis (P < 0.001). Superoxide dismutase and catalase activities decreased, but the reactive oxygen species levels increased as the proportions of P. globosa increased (P < 0.01). The mixture of 50% Chlorella and 50% Phaeocystis positively affected the glutathione content, glutathione peroxidase activity, and generation time of rotifers (P < 0.01). Although P. globosa released toxicants with harmful effects on the growth performance of B. plicatilis, rotifers changed their antioxidant defense system and formed defense phenotypic traits in response to eutrophic conditions.

Progressive effects of single-nucleotide polymorphisms on 16 phenotypic traits based on longitudinal data

Background

There are many research studies have estimated the heritability of phenotypic traits, but few have considered longitudinal changes in several phenotypic traits together.

Objective

To evaluate the progressive effect of single nucleotide polymorphisms (SNPs) on prominent health-related phenotypic traits by determining SNP-based heritability (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$h_{snp}^{2}$$\end{document}hsnp2) using longitudinal data.

Methods

Sixteen phenotypic traits associated with major health indices were observed biennially for 6843 individuals with 10-year follow-up in a Korean community-based cohort. Average SNP heritability and longitudinal changes in the total period were estimated using a two-stage model. Average and periodic differences for each subject were considered responses to estimate SNP heritability. Furthermore, a genome-wide association study (GWAS) was performed for significant SNPs.

Results

Each SNP heritability for the phenotypic mean of all sixteen traits through 6 periods (baseline and five follow-ups) were significant. Gradually, the forced vital capacity in one second (FEV1) reflected the only significant SNP heritability among longitudinal changes at a false discovery rate (FDR)-adjusted 0.05 significance level (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$h_{snp}^{2} = 0.171$$\end{document}hsnp2=0.171, FDR = 0.0012). On estimating chromosomal heritability, chromosome 2 displayed the highest heritability upon periodic changes in FEV1. SNPs including rs2272402 and rs7209788 displayed a genome-wide significant association with longitudinal changes in FEV1 (P = 1.22 × 10⁻⁸ for rs2272402 and P = 3.36 × 10⁻⁷ for rs7209788). De novo variants including rs4922117 (near LPL, P = 2.13 × 10⁻¹⁵) of log-transformed high-density lipoprotein (HDL) ratios and rs2335418 (near HMGCR, P = 3.2 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\times$$\end{document}× 10⁻⁹) of low-density lipoprotein were detected on GWAS.

Conclusion

Significant genetic effects on longitudinal changes in FEV1 among the middle-aged general population and chromosome 2 account for most of the genetic variance.

Electronic supplementary material

The online version of this article (10.1007/s13258-019-00902-x) contains supplementary material, which is available to authorized users.

Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars

BACKGROUND

Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study. A characterization of population structure using easy measurable phenotypic traits could be a preliminary and low-cost approach to elucidate the genetic structure of a population. A potato population of 183 genotypes was evaluated using 4859 high-quality SNPs and 19 phenotypic traits commonly recorded in potato breeding programs. A Bayesian approach, Minimum Spanning Tree (MST) and diversity estimator, as well as multivariate analysis based on phenotypic traits, were adopted to assess the population structure.

RESULTS

Analysis based on molecular markers showed groups linked to the phylogenetic relationship among the germplasm as well as the link with the breeding program that provided the material. Diversity estimators consistently structured the population according to a priori group estimation. The phenotypic traits only discriminated main groups with contrasting characteristics, as different subspecies, ploidy level or membership in a breeding program, but were not able to discriminate within groups. A joint molecular and phenotypic characterization analysis discriminated groups based on phenotypic classification, taxonomic category, provenance source of genotypes and genetic background.

CONCLUSIONS

This paper shows the significant level of diversity existing in a parental population of potato as well as the putative phylogenetic relationships among the genotypes. The use of easily measurable phenotypic traits among highly contrasting genotypes could be a reasonable approach to estimate population structure in the initial phases of a potato breeding program.

Is multiple nest building an adequate strategy to cope with inter-species nest usurpation?

BACKGROUND

Black sparrowhawks (Accipiter melanoleucus) recently colonised the Cape Peninsula, South Africa, where the species faces competition for their nest sites from Egyptian geese (Alopochen aegyptiaca) which frequently usurp black sparrowhawk nests. In this paper, we test the hypothesis that multiple nest building by black sparrowhawks is a strategy to cope with this competitor, based on a 14-year long term data set.

RESULTS

Two main results support the hypothesis: first, the numbers of intact nests per breeding season in black sparrowhawk territories increased as levels of geese interactions increased, specifically when usurpation occurred. Usurpation occurred significantly more often at nests later in the season, and may provide a further explanation for the advancement of the black sparrowhawk breeding season towards earlier breeding attempts which results in an overall extension of the breeding period (over 9 months) that has been found in our study population. Second, nest usurpation had a negative impact on black sparrowhawks' reproductive performance at the 'nest' level, but not at the 'territory' level when multiple nests were available within the same breeding season, suggesting that this strategy was effective for dealing with this competitor. However, our results do not rule out long term negative consequences of these interactions, for example, reduced adult survival rates or reduced lifetime reproductive success, due to the higher energy demand required to build several nests each breeding season.

CONCLUSIONS

Our results suggest that black sparrowhawks avoid direct conflict with this large and aggressive competitor and instead choose the passive strategy in allocating more resources to multiple nest building. Our research further highlights the importance of behavioural plasticity, which might be especially important for city-dwelling species in the face of global urbanisation.

Effects of Starvation in Rock Bream, Oplegnathus fasciatus and Olive Flounder, Paralichthys olivaceus

We assessed the effects of various dietary conditions on the growth, phenotypic traits, and morphometric dimensions of rock bream, Oplegnathus fasciatus and on the morphometric dimensions of sectioned olive flounder, Paralichthys olivaceus. Rock bream in the fed group increased in body weight, standard length, and condition factor, but these parameters decreased significantly for fish in the starved group (P < 0.05). The head connection dimensions of fish in the fed group decreased, while for starved fish there was increase in external morphometric dimensions (P < 0.05). In both species, sectioned morphometric analysis revealed that fish in the fed group had a larger body circumference and cross-cut sectional area, and greater cross-cut section height, relative to the starved group (P < 0.05).

What makes a man a man? Prenatal antennapedia expression is involved in the formation of the male phenotype in Daphnia

Cyclic parthenogenetic organisms show a switch in reproductive strategy from asexual to sexual reproduction upon the occurrence of unfavourable environmental conditions. The sexual reproductive mode involves the production of ameiotic diploid males and the fertilization of meiotic haploid eggs. One beautiful example for this switch between parthenogenesis and sexual reproduction is Daphnia. Male and female Daphnia from the same clone are genetically identical. Morphological differences should therefore only be due to differential gene expression. This differential gene expression leads to sexually dimorphic phenotypes with elongated and moveable (i.e. leg-like) first antennae in males in comparison to females. For other arthropods, it has been demonstrated that the formation of differential morphology of legs and antennae involves the regulation of the Hox gene antennapedia (antp). Here, we show that antp is expressed during the embryogenesis of Daphnia, and that adults contain much lower amounts of antp mRNA than eggs. The eggs of mothers that were treated with the juvenile hormone methyl farnesoate (responsible for the production of male offspring) showed lower expression of antp than parthenogenetically produced female eggs. We therefore conclude that differential antp expression is involved in the molecular pathways inducing the male phenotype of Daphnia.