scholarly journals Restoring fertility in yeast hybrids: Breeding and quantitative genetics of beneficial traits

2021 ◽  
Vol 118 (38) ◽  
pp. e2101242118
Author(s):  
Samina Naseeb ◽  
Federico Visinoni ◽  
Yue Hu ◽  
Alex J. Hinks Roberts ◽  
Agnieszka Maslowska ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Parental Species ◽  
Hybrid Sterility ◽  
Diploid Species ◽  
Hybrid Vigor ◽  
The Road ◽  
High Sugar Concentration ◽  
Interspecies Hybrids ◽  
Beneficial Traits ◽  
Species Specific

Hybrids between species can harbor a combination of beneficial traits from each parent and may exhibit hybrid vigor, more readily adapting to new harsher environments. Interspecies hybrids are also sterile and therefore an evolutionary dead end unless fertility is restored, usually via auto-polyploidisation events. In the Saccharomyces genus, hybrids are readily found in nature and in industrial settings, where they have adapted to severe fermentative conditions. Due to their hybrid sterility, the development of new commercial yeast strains has so far been primarily conducted via selection methods rather than via further breeding. In this study, we overcame infertility by creating tetraploid intermediates of Saccharomyces interspecies hybrids to allow continuous multigenerational breeding. We incorporated nuclear and mitochondrial genetic diversity within each parental species, allowing for quantitative genetic analysis of traits exhibited by the hybrids and for nuclear–mitochondrial interactions to be assessed. Using pooled F12 generation segregants of different hybrids with extreme phenotype distributions, we identified quantitative trait loci (QTLs) for tolerance to high and low temperatures, high sugar concentration, high ethanol concentration, and acetic acid levels. We identified QTLs that are species specific, that are shared between species, as well as hybrid specific, in which the variants do not exhibit phenotypic differences in the original parental species. Moreover, we could distinguish between mitochondria-type–dependent and –independent traits. This study tackles the complexity of the genetic interactions and traits in hybrid species, bringing hybrids into the realm of full genetic analysis of diploid species, and paves the road for the biotechnological exploitation of yeast biodiversity.

scholarly journals Restoring fertility in yeast hybrids: breeding and quantitative genetics of beneficial traits

2021 ◽  
Author(s):  
S. Naseeb ◽  
F. Visinoni ◽  
Y. Hu ◽  
A. J. Hinks Roberts ◽  
A. Maslowska ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Parental Species ◽  
Hybrid Sterility ◽  
Diploid Species ◽  
Hybrid Vigour ◽  
The Road ◽  
High Sugar Concentration ◽  
Beneficial Traits ◽  
Species Specific ◽  
Species Hybrids

AbstractHybrids species can harbour a combination of beneficial traits from each parent and may exhibit hybrid vigour, more readily adapting to new harsher environments. Inter-species hybrids are also sterile and therefore an evolutionary dead-end unless fertility is restored, usually via auto-polyploidisation events. In the Saccharomyces genus, hybrids are readily found in nature and in industrial settings, where they have adapted to severe fermentative conditions. Due to their hybrid sterility, the development of new commercial yeast strains has so far been primarily conducted via selection methods rather than breeding. In this study, we overcame infertility by creating tetraploid intermediates of Saccharomyces inter-species hybrids, to allow continuous multigenerational breeding. We incorporated nuclear and mitochondrial genetic diversity within each parental species, allowing for quantitative genetic analysis of traits exhibited by the hybrids, and for nuclear-mitochondrial interactions to be assessed. Using pooled F12 generation segregants of different hybrids with extreme phenotype distributions, we identified QTLs for tolerance to high and low temperatures, high sugar concentration, high ethanol concentration, and acetic acid levels. We identified QTLs that are species specific, that are shared between species, as well as hybrid specific, where the variants do not exhibit phenotypic differences in the original parental species. Moreover, we could distinguish between mitochondria-type dependent and independent traits. This study tackles the complexity of the genetic interactions and traits in hybrid species, bringing hybrids into the realm of full genetic analysis of diploid species, and paves the road for the biotechnological exploitation of yeast biodiversity.

Characterization of Waterhemp (Amaranthus tuberculatus) × Smooth Pigweed (A. hybridus) F1Hybrids

2006 ◽  
Vol 20 (1) ◽  
pp. 14-22 ◽  
Author(s):  
Federico Trucco ◽  
Tatiana Tatum ◽  
Kenneth R. Robertson ◽  
A. Lane Rayburn ◽  
Patrick J. Tranel
Keyword(s):  
Dna Content ◽  
Parental Species ◽  
Hybrid Sterility ◽  
Field Surveys ◽  
Amaranthus Tuberculatus ◽  
Cytogenetic Analyses ◽  
Morphological Differences ◽  
Species Specific ◽  
Natural Settings ◽  
Smooth Pigweed

In the state of Illinois, waterhemp and smooth pigweed are among the worst agricultural weeds. Previous research shows high potential for hybridization between these two species. However, the actual occurrence of hybrids in natural settings is still uncertain. Morphological similarity between hybrids and waterhemp makes field surveys of hybrids difficult to conduct. The main purpose of this study was to characterize the morphology of waterhemp × smooth pigweed F1hybrids, emphasizing evaluation of characters that may allow for hybrid discrimination in fieldAmaranthuscommunities. Concurrently, the study characterized hybrid reproductive fitness, chromosome number, and DNA content. To accomplish this, hybrids were obtained from field crosses. A species-specific polymorphism in theALSgene was used to verify hybrid identity. Significant differences (α = 0.05) between hybrids and individuals of the parental species were observed for five staminate and five carpellate characters. Of these, five characters differentiated hybrids from waterhemp. However, clustering analyses using these characters indicated that morphological differences were not reliable enough, by themselves, for unambiguous hybrid identification. Also, hybrid homoploidy (2n= 32) with respect to parental species excluded chromosome counts in hybridity determinations. However, DNA content analysis may be used for such purpose. Hybrids had an average of 1.21 pg of DNA per 2C nucleus, a value intermediate to that of parental species. Hybrids produced 3.3 or 0.7% the seed output of parental and sibling waterhemp individuals, respectively. Percent micropollen in hybrids was 95-times greater than in parental species. Hybrid sterility appears to be the most reliable feature for hybrid discrimination when conducting field surveys. However, molecular and cytogenetic analyses as employed in this study may be desired for ultimate identity corroboration.

scholarly journals Micronuclei in germ cells of hybrid frogs from Pelophylax esculentus complex contain gradually eliminated chromosomes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
D. Dedukh ◽  
S. Riumin ◽  
M. Chmielewska ◽  
B. Rozenblut-Kościsty ◽  
K. Kolenda ◽  
...  
Keyword(s):  
Germ Cells ◽  
Parental Species ◽  
Genetic Material ◽  
Single Chromosome ◽  
Water Frog ◽  
Genome Reorganization ◽  
Interspecies Hybrids ◽  
Metaphase Stage ◽  
Pelophylax Esculentus ◽  
Species Specific

Abstract In most organisms, cells typically maintain genome integrity, as radical genome reorganization leads to dramatic consequences. However, certain organisms, ranging from unicellular ciliates to vertebrates, are able to selectively eliminate specific parts of their genome during certain stages of development. Moreover, partial or complete elimination of one of the parental genomes occurs in interspecies hybrids reproducing asexually. Although several examples of this phenomenon are known, the molecular and cellular processes involved in selective elimination of genetic material remain largely undescribed for the majority of such organisms. Here, we elucidate the process of selective genome elimination in water frog hybrids from the Pelophylax esculentus complex reproducing through hybridogenesis. Specifically, in the gonads of diploid and triploid hybrids, but not those of the parental species, we revealed micronuclei in the cytoplasm of germ cells. In each micronucleus, only one centromere was detected with antibodies against kinetochore proteins, suggesting that each micronucleus comprises a single chromosome. Using 3D-FISH with species-specific centromeric probe, we determined the role of micronuclei in selective genome elimination. We found that in triploid LLR hybrids, micronuclei preferentially contain P. ridibundus chromosomes, while in diploid hybrids, micronuclei preferentially contain P. lessonae chromosomes. The number of centromere signals in the nuclei suggested that germ cells were aneuploid until they eliminate the whole chromosomal set of one of the parental species. Furthermore, in diploid hybrids, misaligned P. lessonae chromosomes were observed during the metaphase stage of germ cells division, suggesting their possible elimination due to the inability to attach to the spindle and segregate properly. Additionally, we described gonocytes with an increased number of P. ridibundus centromeres, indicating duplication of the genetic material. We conclude that selective genome elimination from germ cells of diploid and triploid hybrids occurs via the gradual elimination of individual chromosomes of one of the parental genomes, which are enclosed within micronuclei.

SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 948-956 ◽  
Author(s):  
G. Durstewitz ◽  
A. Polley ◽  
J. Plieske ◽  
H. Luerssen ◽  
E. M. Graner ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Oilseed Rape ◽  
Expressed Sequence Tag ◽  
Diploid Species ◽  
Amplicon Sequencing ◽  
Snp Markers ◽  
Snp Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Illumina Goldengate

Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

scholarly journals Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

2017 ◽  
Vol 107 (0) ◽  
Author(s):  
Andrea A. F. Mourão ◽  
Diogo Freitas-Souza ◽  
Diogo T. Hashimoto ◽  
Daniela C. Ferreira ◽  
Fernanda D. do Prado ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Parental Species ◽  
Future Research ◽  
Correct Identification ◽  
Pcr Multiplex ◽  
Pcr Rflp ◽  
Genetic Pattern ◽  
Morphometric Methods ◽  
Species Specific ◽  
Specific Nucleotide

ABSTRACT The hybridization is a widely-discussed issue in several studies with fish species. For some authors, hybridization may be related with diversification and speciation of several groups, or also with the extinction of populations or species. Difficulties to differentiate species and hybrids may be a problem to correctly apply a management of wild species, because hybrid lineages, especially the advanced ones, may resemble the parental species. The genus Cichla Bloch & Schneider, 1801 constitutes an interesting experimental model, considering that hybridization and taxonomic uncertainties hinder a correct identification. Considering these problems, in this study, we developed genetic methodologies and applied meristic and morphometric approaches in wild samples in order to identify species and for test a possible hybridization between Cichla kelberi Kullander & Ferreira, 2006 and Cichla piquiti Kullander & Ferreira, 2006. For this, C. kelberi, C. piquiti and potential hybrid ( carijó) individuals were collected in Paraná and Tietê rivers (SP, Brazil). For meristic and morphometric methods, the individuals were analyzed using the statistical software Pcord 5:31, while for molecular methods, primers for PCR-multiplex were designed and enzyme for PCR-RFLP were selected, under the species-specific nucleotide. All results indicated that the carijó is not an interspecific hybrid, because it presented identical genetic pattern and morphology closed to C. piquiti. Thus, we propose that carijó is a C. piquiti morphotype. In addition, this study promotes a new molecular tool that could be used in future research, monitoring and management programs of the genus Cichla.

scholarly journals Hepatica transsilvanica Fuss (Ranunculaceae) is an Allotetraploid Relict of the Tertiary Flora in Europe – Molecular Phylogenetic Evidence

2020 ◽  
Vol 89 (3) ◽  
Author(s):  
Levente Laczkó ◽  
Gábor Sramkó
Keyword(s):  
Parental Species ◽  
Gene Tree ◽  
Diploid Species ◽  
Nuclear Gene ◽  
Hybrid Origin ◽  
Distribution Area ◽  
Recent Common Ancestor ◽  
Term Survival ◽  
Quaternary Glaciation ◽  
Eastern Carpathians

The <em>Hepatica </em>section <em>Angulosa </em>consists of mainly tetraploid (2<em>n </em>= 28) species that are distributed disjunctly throughout Eurasia. Karyological evidence proves the hybrid origin of the polyploid species of this section. <em>Hepatica transsilvanica </em>is a member of this species group with a conspicuous distribution restricted to the Eastern Carpathians. Based on genome size and cytotypes, the paternal parent of <em>H. transsilvanica </em>is described to be the only diploid species in section <em>Angulosa</em>, <em>H. falconeri</em>. The maternal species is hypothesized to be <em>H. nobilis</em>, a European species with entirely lobed leaves and a wider distribution area. Although the hybrid origin of <em>H. transsilvanica </em>is well documented by karyological evidence, the time of hybridization has never been studied. By using sequences of both the nuclear and plastid genome, we reconstructed the phylogenetic relationships and divergence times of <em>H. transsilvanica </em>and its parental species. The identity of the parental species is corroborated by discordant gene tree topologies of the nrITS and plastid sequences. Moreover, both gene copies of the parental species could be identified with the low-copy nuclear gene, <em>MLH1</em>. Divergence dating analysis using Bayesian phylogenetic methods strongly supported the long-term survival of <em>H. transsilvanica </em>in the Southeastern Carpathians, as the most recent common ancestor of the hybrid and parent species existed not later than the beginning of the Pleistocene, ca. 3 million years ago. These results not only highlight the biogeographic importance of the Southeastern Carpathians in the Quaternary glaciation periods, but also emphasize that Tertiary lineages could have survived in a Central European cryptic refugium.

scholarly journals Metabolic output defines Escherichia coli as a health-promoting microbe against intestinal Pseudomonas aeruginosa

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Theodoulakis Christofi ◽  
Stavria Panayidou ◽  
Irini Dieronitou ◽  
Christina Michael ◽  
Yiorgos Apidianakis
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Short Chain Fatty Acids ◽  
High Titre ◽  
Important Indicator ◽  
High Sugar Concentration ◽  
Intestinal Pathogens ◽  
Health Promoting ◽  
Species Specific ◽  
Metabolic Output

Abstract Gut microbiota acts as a barrier against intestinal pathogens, but species-specific protection of the host from infection remains relatively unexplored. Although lactobacilli and bifidobacteria produce beneficial lactic and short-chain fatty acids in the mammalian gut, the significance of intestinal Escherichia coli producing these acids is debatable. Taking a Koch’s postulates approach in reverse, we define Escherichia coli as health-promoting for naturally colonizing the gut of healthy mice and protecting them against intestinal colonization and concomitant mortality by Pseudomonas aeruginosa. Reintroduction of faecal bacteria and E. coli in antibiotic-treated mice establishes a high titre of E. coli in the host intestine and increases defence against P. aeruginosa colonization and mortality. Strikingly, high sugar concentration favours E. coli fermentation to lactic and acetic acid and inhibits P. aeruginosa growth and virulence in aerobic cultures and in a model of aerobic metabolism in flies, while dietary vegetable fats - not carbohydrates or proteins - favour E. coli fermentation and protect the host in the anaerobic mouse gut. Thus E. coli metabolic output is an important indicator of resistance to infection. Our work may also suggest that the lack of antimicrobial bacterial metabolites in mammalian lungs and wounds allows P. aeruginosa to be a formidable microbe at these sites.

scholarly journals A high-throughput method for unbiased quantitation and categorization of nuclear morphology

2019 ◽  
Vol 100 (5) ◽  
pp. 1250-1260 ◽  
Author(s):  
Benjamin Matthew Skinner ◽  
Claudia Cattoni Rathje ◽  
Joanne Bacon ◽  
Emma Elizabeth Philippa Johnson ◽  
Erica Lee Larson ◽  
...  
Keyword(s):  
Morphometric Analysis ◽  
Hybrid Sterility ◽  
Inbred Strains ◽  
Mouse Strains ◽  
Nuclear Morphology ◽  
Analysis Program ◽  
Cell Type ◽  
High Throughput Method ◽  
Sperm Development ◽  
Species Specific

Abstract The physical arrangement of chromatin in the nucleus is cell type and species-specific, a fact particularly evident in sperm, in which most of the cytoplasm has been lost. Analysis of the characteristic falciform (“hook shaped”) sperm in mice is important in studies of sperm development, hybrid sterility, infertility, and toxicology. However, quantification of sperm shape differences typically relies on subjective manual assessment, rendering comparisons within and between samples difficult. We have developed an analysis program for morphometric analysis of asymmetric nuclei and characterized the sperm of mice from a range of inbred, outbred, and wild-derived mouse strains. We find that laboratory strains have elevated sperm shape variability both within and between samples in comparison to wild-derived inbred strains, and that sperm shape in F1 offspring from a cross between CBA and C57Bl6J strains is subtly affected by the direction of the cross. We further show that hierarchical clustering can discriminate distinct sperm shapes with greater efficiency and reproducibility than even experienced manual assessors, and is useful both to distinguish between samples and also to identify different morphological classes within a single sample. Our approach allows for the analysis of nuclear shape with unprecedented precision and scale and will be widely applicable to different species and different areas of biology.

scholarly journals Genetics of morphological differences and hybrid sterility between Drosophila sechellia and its relatives

1991 ◽  
Vol 57 (2) ◽  
pp. 113-122 ◽  
Author(s):  
Jerry A. Coyne ◽  
John Rux ◽  
Jean R. David
Keyword(s):  
Genetic Analysis ◽  
X Chromosome ◽  
Sibling Species ◽  
Male Genitalia ◽  
Hybrid Sterility ◽  
Drosophila Sechellia ◽  
Ovariole Number ◽  
The Difference ◽  
Male Hybrid ◽  
Morphological Differences

SummaryWe conducted classical genetic analysis of the difference in male genitalia and hybrid sterility between the island-dwelling sibling species Drosophila sechellia and D. mauritiana. At least two loci (one on each autosome) are responsible for the genital difference, with the X chromosome having no significant effect. In contrast, male hybrid sterility is caused by at least four gene loci distributed among all major chromosomes, with those on the X chromosome having the largest effect.We also show that the large difference in ovariole number between D. sechellia and its mainland relative D. simulans is due to at least two gene substitutions, one on each major autosome. The X and the left arm of the second chromosome, however, have no significant effect on the character. This implies that the evolution of reduced ovariole number involved relatively few gene substitutions.These results extend previous findings that morphological differences between Drosophila species are caused by genes distributed among all chromosomes, while hybrid sterility and inviability are due primarily to X-linked genes. Because strong X-effects on male sterility have been found in all three pairwise hybridizations among D. simulans, D. sechellia and D. mauritiana, these effects must have evolved at least twice independently.

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