Genetic Variation of a Lentil (Lens culinaris) Landrace during Three Generations of Breeding

Genetic differentiation between 40 lentil genotypes was tested using molecular markers. The genotypes were produced from a Greek landrace of commercial interest via the honeycomb breeding methodology, i.e., single-plant selection in the absence of competition, across three successive pedigree generations. The selected genotypes from each generation were examined for genetic relationships using 15 SSR molecular markers with HRM analysis. As expected, low variation among consecutive generations at the level of 2.5–7.7% was detected. Analysis of molecular variance (AMOVA) revealed that partitioning of this variation was at higher percentage within each generation’s population than between them. Population structure analysis indicated that ongoing selection could effectively shift the allelic composition in each generation. The applied honeycomb breeding methodology that effectively improved progeny yield and seed quality increased the percentage of favorable alleles altering allelic composition but not eliminating genetic variation of the breeding population.

Annual climatic fluctuations and short-term genetic variation in the eastern spadefoot toad

In addition to variations on the spatial scale, short- and long-term temporal variations, too, can impose intense selection on the overall genetic diversity and composition of a population. We hypothesized that the allelic composition in populations of the eastern spadefoot toad (Pelobates syriacus) would change among successive years in accordance with the short-term changes in environmental conditions. Surprisingly, the effect of short-term climate fluctuations on genetic composition have rarely been addressed in the literature, and to our knowledge the effect of annual climatic fluctuations have not been considered meaningful. Our findings show that climatic variation among successive years, primarily the amount of rainfall and rainy days, can significantly alter both microsatellite allelic composition and diversity. We suggest that environmental (i.e. fluctuating) selection is differential across the globe, and that its intensity is expected to be greatest in regions where short-term climatic conditions are least stable.

Allelic composition of carotenoid metabolic genes in 13 founders influences carotenoid composition in juice sac tissues of fruits among Japanese citrus breeding population

To enrich carotenoids, especially β-cryptoxanthin, in juice sac tissues of fruits via molecular breeding in citrus, allele mining was utilized to dissect allelic variation of carotenoid metabolic genes and identify an optimum allele on the target loci characterized by expression quantitative trait (eQTL) analysis. SNPs of target carotenoid metabolic genes in 13 founders of the Japanese citrus breeding population were explored using the SureSelect target enrichment method. An independent allele was determined based on the presence or absence of reliable SNPs, using trio analysis to confirm inheritability between parent and offspring. Among the 13 founders, there were 7 PSY alleles, 7 HYb alleles, 11 ZEP alleles, 5 NCED alleles, and 4 alleles for the eQTL that control the transcription levels of PDS and ZDS among the ancestral species, indicating that some founders acquired those alleles from them. The carotenoid composition data of 263 breeding pedigrees in juice sac tissues revealed that the phenotypic variance of carotenoid composition was similar to that in the 13 founders, whereas the mean of total carotenoid content increased. This increase in total carotenoid content correlated with the increase in either or both β-cryptoxanthin and violaxanthin in juice sac tissues. Bayesian statistical analysis between allelic composition of target genes and carotenoid composition in 263 breeding pedigrees indicated that PSY-a and ZEP-e alleles at PSY and ZEP loci had strong positive effects on increasing the total carotenoid content, including β-cryptoxanthin and violaxanthin, in juice sac tissues. Moreover, the pyramiding of these alleles also increased the β-cryptoxanthin content. Interestingly, the offset interaction between the alleles with increasing and decreasing effects on carotenoid content and the epistatic interaction among carotenoid metabolic genes were observed and these interactions complexed carotenoid profiles in breeding population. These results revealed that allele composition would highly influence the carotenoid composition in citrus fruits. The allelic genotype information for the examined carotenoid metabolic genes in major citrus varieties and the trio-tagged SNPs to discriminate the optimum alleles (PSY-a and ZEP-e) from the rest would promise citrus breeders carotenoid enrichment in fruit via molecular breeding.

INVESTIGATION OF THE ALLELIC COMPOSITION OF THE MA-3 MICROSATELLITE LOCUS IN SABLE (MARTES ZIBELLINA L., 1758) OF THE MIDDLE AMUR REGION: ANALYSIS OF THE COLLECTIONS OF SUCCESSIVE HUNTING SEASONS

The authors investigated the allele microsatellite locus Ma-3 composition in the Middle Amur Region sable (Martes zibellina). Three subpopulations of animals from the Bureinsky Highlands (Magan, Sutyr and Kamenushka), as well as one from the western macro slope of the Sikhote-Alin ridge (Manoma) were analyzed. The genetic material was collected for the hunting seasons of 2011/2012 – 2017/2018. Subpopulations of the northern (Magan) and middle (Sutyr) parts of the Bureinsky ridge were most similar to each other in their allele composition In the subpopulation of the Bureinsky Highlands southern part (Kamenushka) some slight differences were found. In the Manoma subpopulation, the specific allele 129 was found in hunting catches of 2012-2013 and 2017-2018. The specific allele presence in this subpopulation has proved some geographic isolation between the Sikhote Alin and the Bureinsky Highlands sable populations.

Tracing the evolution of aneuploid cancers from multiregional sequencing

To understand the evolutionary dynamics of cancer, clonal deconvolution of mutational landscapes across multiple biopsies from the same patient is crucial. However, the frequencies of mutated alleles are often distorted by variation in copy number of mutated loci as well as the purity across samples. We present a semi-supervised algorithm that normalizes for purity and incorporates allelic composition with bulk sequencing to reliably segregate clonal/subclonal variants even at low sequencing depth (∼50x). In presence of at least one tumor sample with >70% purity, it deconvolves samples down to ∼40% purity, allowing robust tracking of mutated cell populations through cancer evolution.

Identification of allelic combinations of the Ppd-D1, Vrn-A1, Vrn-B1 and Vrn-D1 genes in common wheat lines obtained in the National Center of Grain named after P. P. Lukyanenko

An analysis of the allelic composition of the genes determining photoperiodic sensitivity (Ppd-D1) and the need for vernalization (Vrn-A1, Vrn-B1, Vrn-D1) was carried out in 286 common wheat lines obtained in the National Center of Grain named after P. P. Lukyanenko with the use of allele-specific primers. The analyzed samples were distributed over 21 haplotypes; the dominant allele of the Ppd-D1a gene prevailed in the studied material. 123 lines of common wheat carry a combination of D-RRD alleles. The lines that can be attributed to the group of alternate wheat (R-RDR, R-RRD) were identified. All studied samples carry the recessive allele of at least one VRN1 gene.

Allelic composition at GLU genes in a collection of spring wheat germplasm

For HMW-GS, a total of 16 different subunits and 30 allelic haplotypes were identified. The expression of HMW-GS ranged from 3 to 5 per genotype instead of 6 per genotype, revealing the phenomenon of gene silencing. The 2* was the most frequent subunit for Glu-A1 locus and was found in 52.45% lines. Eight subunits were identified for Glu-B1 locus. Five subunit pairs i.e. 6+8, 7+8, 7+9, 13+16 and 17+18 were present in the germplasm. Some single subunits i.e. 6, 7, 8 and 20 were also found. Subunit pair 17+18 was the most frequent with a partial frequency of 32.17%. For Glu-D1, four subunit pairs i.e. 2+12, 5+10, 2+11 and 5+11 were observed. The 5+10 was the most frequent subunit for Glu-D1 and was present in 65.03% lines. The 2+12 subunit pair was identified in 34.97% lines. For Glu3 loci 18 LMW subunits were identified. For Glu-A3, five subunits i.e. b, c, d, e and g were identified. Eight subunits i.e. b, c, d, f, g, h, i and j were identified for Glu-B3 locus. Four subunits i.e. a, b, c and l were identified for Glu-D3 locus.