Hybrid Populations Research Articles

Investigation of genome-wide InDel distribution and segregation in Populus with restriction-site associated DNA sequencing data

Insertion or deletion polymorphism (InDel) is one of the main genetic variations in plant genomes. However, there are few studies on InDels across the whole genome in Populus. In this study, we investigated genome-wide InDels in Populus deltoides and Populus simonii and InDel segregation in their F1 hybrid population with restriction-site associated DNA sequencing (RAD-seq) data. A total of 119,066 InDels were identified in P. deltoides and P. simonii according to the reference genome of Populus trichocarpa, including 58,532 unique InDels in P. deltoides, 54,469 unique InDels in P. simonii, and 6,065 common InDels in both. Meanwhile, the distribution of these InDels was analyzed along chromosomes, indicating that the distribution patterns for both species were largely similar, but the average InDel density was slightly higher in P. deltoides than in P. simonii. GO annotation and enrichment analysis of those genes harboring InDels showed the same patterns between the two poplar species. It is interesting to find that the ratio (~ 46%) of the common InDels within genes to all common InDels was higher than that of the InDels within genes to all InDels in P. deltoides (~ 35%) or in P. simonii (~ 34%), possibly indicating that those InDels are more conservative between poplar species. Moreover, investigation of the InDel segregation patterns demonstrated that a large number of Mendelian InDels could be selected for genetic mapping in the F1 hybrid population. RAD-seq provides genome-wide insights into the InDel distributions in P. deltoides and P. simonii and the segregation patterns in their progeny, providing valuable genomic variation information for genetic and evolutionary studies in Populus.

Phenolic Compounds in Black Grape by the Electronic and Thermochemical Studies

This investigation analyzes the effects of light and genotype on the biosynthesis of anthocyanins. The applied plant material, including dye grape varieties, accumulates anthocyanins in the skin and the pulp and hybrid populations. Anthocyanins are secondary plant metabolites with the response of most of the red to purple pigmentation existing in fruits, vegetables, and flowers. During grape berry development, these compounds are accumulated from maturation until ripening and are responsible for pigmentation found in red skin berries. Several cations linked to anthocyanins in H2O molecules have been investigated for studying the color difference of various compounds in the low limitations of pH value. In this accomplishment, cations attached to Mal, Peo, Del, Pet, and Cya in water has been simulated, converting flavylium cations to the blue quinonoidal bases at a lower amount of pH using the IR approach by installing the beer-lambert law for getting the physicochemical properties of absorbance, intensity and of the structures. The changes of enthalpy between complexes of anthocyanins-cations have been discussed due to carbonyl groups and double bonds by the (B)-ring chelated of cyanidin, delphinidin, and petunidin anthocyanins in different media of gas and water which illustrates the stability and color of anthocyanin-cations chelated to Mal, Peo, Del, Pet, and Cya colorful pigments in a weakly acidic medium.

Imbalanced segregation of recombinant haplotypes in hybrid populations reveals inter- and intrachromosomal Dobzhansky-Muller incompatibilities.

Dobzhansky-Muller incompatibilities (DMIs) are a major component of reproductive isolation between species. DMIs imply negative epistasis and are exposed when two diverged populations hybridize. Mapping the locations of DMIs has largely relied on classical genetic mapping. Approaches to date are hampered by low power and the challenge of identifying DMI loci on the same chromosome, because strong initial linkage of parental haplotypes weakens statistical tests. Here, we propose new statistics to infer negative epistasis from haplotype frequencies in hybrid populations. When two divergent populations hybridize, the variance in heterozygosity at two loci decreases faster with time at DMI loci than at random pairs of loci. When two populations hybridize at near-even admixture proportions, the deviation of the observed variance from its expectation becomes negative for the DMI pair. This negative deviation enables us to detect intermediate to strong negative epistasis both within and between chromosomes. In practice, the detection window in hybrid populations depends on the demographic scenario, the recombination rate, and the strength of epistasis. When the initial proportion of the two parental populations is uneven, only strong DMIs can be detected with our method unless migration prevents parental haplotypes from being lost. We use the new statistics to infer candidate DMIs from three hybrid populations of swordtail fish. We identify numerous new DMI candidates, some of which are inferred to interact with several loci within and between chromosomes. Moreover, we discuss our results in the context of an expected enrichment in intrachromosomal over interchromosomal DMIs.

Cross-Species Amplification and Variability of Microsatellite DNA Markers in Domesticated Indonesian Mahseer; A Case Study with Tor soro, Tor douronensis and their Interspecific Hybrids

Indonesian mahseer (Tor spp.) are freshwater species of high economic, cultural, and conservatory values. Owing to their high values and environmental degradation, the population of Tor fish gradually decreased, and domestication efforts have been made to conserve the population. This study was aimed to assess the cross-species amplification and microsatellite genetic diversity in Indonesian mahseer Tor soro (SS), Tor douronensis (DD), and their interspecific hybrids using primers developed for Tor putitora. Eleven primer sets were used to test for amplifiability and screen genetic diversity in 40 progenies derived from those three groups. Results showed that seven primer sets (64%) successfully amplified loci. Genetic screening using the three most consistently amplifying primers showed that the number of alleles in the three populations was low, ranging from 2 to 5 alleles. The observed heterozygosity (HO) was high ranging from 0.650 to 0.789, and the fixation index (FIS) was negative, indicating heterozygosity excess. In line with other parameters, the P-values of the HW parameter of several loci-population combinations were significantly departed from equilibrium (P <0.05). A few private alleles were observed in parental line DD and the hybrids. Overall, the cross-species primers developed from T. putitora were able to amplify loci in T. soro, T. douronensis and their hybrids and genetic diversity in the hybrid population was slightly higher than those in parental lines. Possible factors driving the phenomena and practical implications of these findings on the conservation measures are discussed.

PHENOMENON OF TRANSGRESSION VARIABILITY IN POPULATIONS OF VARIOUS TYPES OF HEMP INTERVARIETAL HYBRIDS

The article deals with the issues of the phenomenon of transgression variability in populations of various types of hemp intervarietal hybrids. The study of the first generation of various types of intervarietal hemp hybrids showed that transgression trait is observed in most traits available for study. Studies showed that the height of intervarietal hemp hybrid plants transgresses within a fairly wide range, depending on the types of crossing. Concurrently, the genotypes of parental components have a great influence on the degree and frequency of tall and short-stemmed plants. So, in case of direct crossing of forms close in plant height (Glukhovskaya-10 and Odnodomnaya-2, YUS-9 and Poltavskaya-3), a population with biotypes exceeding the best parent by 18-19% is created in the offspring. The occurrence of such plants in this case is significant (12-16%). Crossing of components that differ greatly in plant height (YUS-9 and Odnodomnaya-2, Glukhovskaya-10 and Poltavskaya-3) shows a degree of transgression of 13-14% and a frequency of 9-10%. There is a transgression of some productivity elements in populations of various types of intervarietal hemp hybrids. The highest rates of transgression are revealed by the stem weight of one plant. The splitting nature of the first generation of simple intervarietal hybrids depends on the genotypes of the parental forms. Thus, when crossing Glukhovskaya-10 and Odnodomnaya-2 varieties, which are identical in stem weight, a population of biotypes, exceeding the best parent by 25% is created. The occurrence of such plants in this case is significant (24%). When crossing forms of YUS-9 and Odnoedomnaya-2, contrasting in stem weight, the degree of transgression is 18%, and the frequency is 15%. Transgression practically does not occur in the offspring of backcross hybrids. Therefore, the best biotypes in terms of a complex of traits, isolated in the offspring of first-generation hybrids, should be used to obtain complex hybrid populations. Complex hybrid populations are a valuable source material and can be the parent of a variety.

Comparison of immune defense and antioxidant capacity between broodstock and hybrid offspring of juvenile shrimp (Macrobrachium nipponense): Response to acute ammonia stress

Ammonia is a major environmental pollutant in the aquatic system that poses a great threat to the health of shrimp. Macrobrachium nipponense, as one of the large-yield farmed shrimp, is facing germplasm degradation. Genetic improvement through hybridization is one of the effective methods to solve this problem. However, there are few studies on the effects of ammonia nitrogen on the germplasm resources of M.nipponense. In this study, the broodstock populations (Dianshan, DS) and hybrid offspring (DS ♀×CD [Changjiang, CJ ♂×Dongting, DT ♀], SCD) were exposed to 0, 5, or 20mg/L of ammonia for 96h. The survival rate of the SCD group was greater than the DS group, although there were no significant differences in weight gain rate and length gain rate (p>0.05). The number of positive cells and apoptosis rates in the DS group were significantly greater than in the SCD group after ammonia exposure (p<0.05). As the ammonia concentration increased, the antioxidant enzyme activities in the SCD group were significantly higher than DS group, while the hepatotoxicity enzyme activities in the SCD group were significantly lower than DS group (p<0.05). The trends in the expression of antioxidant- and immune-related genes were generally consistent with the activities of antioxidant enzymes. Our study found that the hybrid population had stronger stress resistance than their parent populations at the same ammonia concentration. This study confirms our speculation that hybrid population has a greater advantage in antioxidant immunity, which also provides reference for the follow-up study of chronic ammonia toxicity.

Сучасна селекція високоврожайних сортів тритикале з поліпшеною якістю зерна

Goal. To study genotypes of hexaploid triticale using systematic ecological tests in contrast conditions and create new medium and low-stem lines with high potential productivity and improved grain quality, form multi-line varieties with the straw length of 80 – 120 cm, the yield of 9.5 – 13.5 t/ha, high quality of gluten, dough and bread. Methods. The object of research was: samples of winter and spring triticale, soft and durum wheat, rye of different geographical and genetic origins, intergeneric, interspecific and intraspecific hybrids, as well as populations created on their basis. The sowing rate was 4.5 million similar seeds per 1 hectare, the plot area was 10 m2. Intraspecific hybridization was used in winter triticale breeding with the assessment of grain and bread quality of multilinear varieties. Hybrid populations were created by crossing hexaploid triticales, which differed in origin and type of development. Results. The use of the method of intraspecific hybridization in combination with long-term trials of hybrid populations and lines in contrast conditions allowed the creation of new varieties of winter triticale. Research work was carried out on the creation of triticale cultivars of a fundamentally new type, which differ in the areas of use, are short-stemmed and high-quality grain. Triticale varieties created in recent years in research institutions of the NAAS had high productivity potential, comprehensive immunity to major diseases, and a large volume of bread without improvers (800 ml) with a total baking score of 9 points. Conclusions. Genotypes of hexaploid triticale were studied using systematic ecological tests in contrast conditions, and new medium and low stem lines with high potential productivity and improved grain quality were created, multilinear varieties were formed with a straw length of 80 – 120 cm, a yield of 9.5 – 13.5 t/ha, high-quality gluten, dough and bread.

High-resolution bin-based linkage mapping uncovers the genetic architecture and heterosis-related loci of plant height in indica-japonica derived populations.

Plant height (PH) is an important trait affecting the plant architecture, seed yield, and harvest index. However, the molecular mechanisms underlying PH heterosis remain unclear. In addition, useful PH-related genes must be urgently identified to facilitate ideal plant architecture breeding in rice (Oryza sativa L.). In the present study, to explore rice quantitative trait loci (QTLs) and heterosis-related loci of PH in rice, we developed a high-generation (>F15 ) population of 272 recombinant inbred lines (RIL) from a cross of two elite varieties, Luohui 9 (indica/xian) × RPY geng (japonica/geng), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA [indica] and Z7A [japonica]). Using deep resequencing data, a high-density genetic map containing 4758 bin markers was constructed, with a total map distance of 2356.41 cM. Finally, 31 PH-related QTLs for different PH component lengths or tiller numbers across five seasons were identified. Two major environment-specific PH QTLs were stably detected in Hainan (qPH-3.1) or Hubei (qPH-5.1), which have undergone significant functional alterations in rice with changes in geographical environment. Based on comparative genomics, gene function annotation, homolog identification, and existing literature (pioneering studies), candidate genes for multiple QTLs were fine-mapped, and the candidate genes qPH-3.1 and qPH-5.1 for PH were further validated using CRISPR-Cas9 gene editing. Specifically, qPH-3.1 was characterized as a pleiotropic gene, and the qPH-3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers. Importantly, 10 PH heterosis-related QTLs were identified in the testcross populations, and a better-parent heterosis locus (qBPH-5.2) completely covered qPH-5.1. Furthermore, the cross results of fixed-genotype RILs verified the dominant effects of qPH-3.1 and qPH-5.1. Together, these findings further our understanding of the genetic mechanisms of PH and offer multiple highly reliable gene targets for breeding rice varieties with ideal architecture and high yield potential in the immediate future.

Four-Year and Five-Developing-Stage Dynamic QTL Mapping for Tiller Number in the Hybrid Population of Agropyron Gaertn.

Tiller number (TN) is an important agronomic trait affecting gramineous crop yield. To understand the static and dynamic information of quantitative trait locus (QTLs) controlling TN of Agropyron Gaertn., both the unconditional and conditional quantitative trait loci (QTL) mapping of TN were conducted using a cross-pollinated (CP) hybrid population with a total of 113 plant lines from the cross between Agropyron cristatum (L.) Gaertn. Z1842 and Allium mongolicum Keng Z2098, based on the phenotypic data of TN at five developmental stages [i.e., recovering stage (RS), jointing stage (JS), heading stage (HS), flowering stage (FS), and maturity stage (MS)] in 4 years (i.e., 2017, 2018, 2020, and 2021) and the genetic map constructed of 1,023 single-nucleotide polymorphism (SNP) markers. Thirty-seven QTLs controlling TN were detected using two analysis methods in 4 years, which were distributed in six linkage groups. Each QTL explained 2.96–31.11% of the phenotypic variation, with a logarithum of odds (LOD) value of 2.51–13.95. Nine of these loci detected both unconditional and conditional QTLs. Twelve unconditional major QTLs and sixteen conditional major QTLs were detected. Three relatively major stable conditional QTLs, namely, cQTN1-3, cQTN1-5, and cQTN4-1, were expressed in 2020 and 2021. Meantime, two pairs of major QTLs cQTN1-5 and qTN1-4 and also cQTN2-4 and qTN2-3 were located at the same interval but in different years. Except for qTN2-2 and qTN3-5/cQTN3-5, other thirty-four QTLs were first detected in this study. This study provides a better interpretation of genetic factors that selectively control tiller at different developmental stages and a reference for molecular marker-assisted selection in the related plant improvement.

Abstract P5-12-06: Msc engulfing by triple negative breast cancer cells induces a hybrid cell population with senescence

Abstract Introduction: Triple negative breast cancer (TNBC) represents ~15% of all breast cancers. The TNBC subtype is characterized by the absence of estrogen and progesterone receptors and of ErbB2. Biologically, it is well recognized that TNBC has a more aggressive phenotype compared to other subtypes, offering limited treatment options and a worse clinical outcome. Tumor cells, through production of paracrine and endocrine molecules, can recruit mesenchymal stem/stromal cells (MSCs) from the bone marrow and adipose tissue to the tumor microenvironment. MSCs, reside mainly in the bone marrow and in adipose tissue. MSCs may exert a crucial role in tumor development and progression, by increasing stemness of tumor cells and promoting extracellular matrix remodeling, cell migration and invasion, neo-angiogenesis, and drug resistance. We have shown that breast cancer cells (BCCs) can engulf MSCs and induce an aggressive phenotype and increased metastasis. The mechanisms through which MSC engulfment occurs and the generated phenotypes need to be investigated. In this study, we tested the hypothesis that MSC engulfment by BCC cells may result in a hybrid tumor cell population with features of cell senescence, a well-recognized mechanism of tumor progression and recurrence. Methods: We employed MDA-MB-231 TNBC cells and patient-derived MSCs developed and validated in our lab. MDA-MB-231 were labeled with DsRED (231- DsRED) and MSCs were not labeled. Single culture of MDA-MB-231, MSCs, and MDA-MB-231/MSC co-cultures (1:1 ratio) were subjected to SA-β-galactosidase activity assay, flow cytometry, and immunofluorescence to detect and quantify the percentage of hybrid and senescence cells. SA-β-galactosidase activity assay was assessed using Senescence-associated β-galactosidase Staining Kit. For each sample of the single cultures and co-cultures, 10 randomly chosen fields were photographed using a camera-equipped bright field microscope (Olympus). Data was plotted as the percentage of cells with β-galactosidase activity (blue cells). We performed flow cytometry to detect β-galactosidase activity in MSCs and in DsRED-231 in single cultures or co-cultures. Immunofluorescence assay was performed to evaluate β-galactosidase activity in the same conditions previously described. Results: Our studies identified the emergence of a hybrid cell population in the co-cultures of MDA-MB-231 and MSCs cells. The hybrid population contained a significantly higher percentage of senenscent cells compared to 231 and MSCs (44%, 10.23%, and 14%, respectively, t test 0.001). These results were confirmed by immunofluorescence analysis for β-galactosidase, DsRed and DAPI in situ. Conclusion: These results highlight that MSCs engulfment by TNBC cells induces the formation of senescent hybrid breast cancer cells, which may explain their survival advantage. Studies are under way to investigate if the senescent phenotype of hybrid cells is influenced by EMT-MET states and its role in TNBC chemoresistance. Citation Format: Alessandro Paolì, Maria Elena Gonzalez, Loredana Mauro, Sebastiano Andò, Celina Graciela Kleer. Msc engulfing by triple negative breast cancer cells induces a hybrid cell population with senescence [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-12-06.

Abstract P5-06-06: Hybrid cells generated by Mesenchymal Stem/Stromal Cell Engulfment enhance breast cancer metastasis upon Doxorubicin treatment in mouse model

Abstract Introduction: Our previous findings evidenced that BCCs engulf MSCs in clinical samples of breast cancer metastasis. Among the BCC-engulfing MSCs, we observed that some of them retain some markers of MSCs, resulting in the generation of hybrid cancer cell population. However, the mechanisms of hybrid cancer cell formation and the phenotypic features of hybrid cancer cells are still unclear. Here, we tested the hypothesis that hybrid cancer cells may acquire in vivo a dormant phenotype, with an increased survival advantage and chemoresistant features. Method: MSC labeled with DsRED (DsRED-MSC) were cultured with MDA-MB-231 labeled with GFP (GFP-231) to generate a hybrid cell-enriched co-culture. Live imaging microscopy, flow cytometry, cytokine array and western blot were used to characterize the hybrid cancer cells. GFP-231 were incubated with phRodo labeled MSC and subjected to phagocytosis assay. In the co-culture of DsRED-MSC with GFP-231 treated with Doxorubicin (Doxo) or untreated, we analyzed the percentage of DsRED+/GFP+ hybrid population. Hybrid-enriched co-culture or GFP-231 in single culture labeled with firefly luciferase were intracardially injected in NOD/SCID mice and monitored for metastases by bioluminescence imaging (BLI), upon Doxo treatment. After collecting the tissues at necropsy, metastases were identified by GFP fluorescence microscopy. Results: In co-cultures, DsRED+/GFP+ hybrid cells had a higher percentage of Ki-67 low in G1 and polyploidy compared to GFP-231+ cells. Hybrid cancer cells have a distinct cytokine profile than control BCCs with increased levels of senescence-associated secretory phenotype (SASP) factors. Hybrid cancer cell formation occurs through a phagocytosis-like mechanism, which involves WNT5A and MSR1. Doxo treatment increased the percentage of DsRED+/GFP+ hybrid cells, whereas reduced the percentage of GFP-231+ cells. In animal study, we observed a lower qualitative BLI intensity in mice injected with hybrid cell-enriched co-cultures compared to control. Doxo treatment increased the metastatic burden in mice inoculated with hybrid cell-enriched co-cultures compared to untreated Conclusions: MSC engulfment by BCCs results in a hybrid multinucleated cell population. Hybrid cells acquire a dormant phenotype characterized by a higher percentage of Ki-67low cells in G1 and a senescent phenotype compared to controls. Hybrid-cell-enriched co-cultures established less metastasis compared to control in vivo, but became resistant and acquire the ability to form metastasis upon doxo treatment. Citation Format: Giuseppina Augimeri, Maria E. Gonzalez, Daniela Bonofiglio, Sebastiano Andò, Celina G. Kleer. Hybrid cells generated by Mesenchymal Stem/Stromal Cell Engulfment enhance breast cancer metastasis upon Doxorubicin treatment in mouse model [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-06-06.

Study of hybrid and backcross abalone populations uncovers trait separation and their thermal resistance capacity

Hybridization and backcrossing are classical breeding methods that can effectively improve the genetic characteristics of organisms through heterosis. The hybrid abalone (Haliotis discus hannai ♀ × H. fulgens ♂, DF) and backcrosses are cultured on a large scale due to their high survival rates under heat stress in summer. The thermal resistance of purebreds, hybrid F1 and backcross populations were evaluated through Arrhenius break temperature (ABT) of cardiac performance in this study. The results showed that the hybrid F1 had the best thermal resistance, and the ABT gradually decreased with the increase in recurring number. In addition, a growth experiment of DD × DF (H. discus hannai ♀ × DF ♂) populations showed that DD × DF-Y (presence of black spots in the visceral mass of DD × DF) grew faster than DD × DF-N (absence of spots in the visceral mass of DD × DF) (p < 0.05), but the ABT of DD × DF-Y was lower than that of DD × DF-N (p < 0.05). The results suggest that the presence or absence of black spots in the visceral mass could be used as a breeding trait for the thermal resistance and growth of backcross abalone. This study provides basic data for further study of the response of abalone to heat stress for the healthy and sustainable development of the abalone industry.

Identification of Putative Markers of Non-infectious Bud Failure in Almond [Prunus dulcis (Mill.) D.A. Webb] Through Genome Wide DNA Methylation Profiling and Gene Expression Analysis in an Almond × Peach Hybrid Population.

Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important nut crop susceptible to the genetic disorder, Non-infectious Bud Failure (NBF). Despite the severity of exhibition in several prominent almond cultivars, no causal mechanism has been identified underlying NBF development. The disorder is hypothesized to be associated with differential DNA methylation patterns based on patterns of inheritance (i.e., via sexual reproduction and clonal propagation) and previous work profiling methylation in affected trees. Peach (Prunus persica L. Batsch) is a closely related species that readily hybridizes with almond; however, peach is not known to exhibit NBF. A cross between an NBF-exhibiting ‘Carmel’ cultivar and early flowering peach (‘40A17’) produced an F1 where ∼50% of progeny showed signs of NBF, including canopy die-back, erratic branching patterns (known as “crazy-top”), and rough bark. In this study, whole-genome DNA methylation profiles were generated for three F1 progenies exhibiting NBF and three progenies considered NBF-free. Subsequent alignment to both the almond and peach reference genomes showed an increase in genome-wide methylation levels in NBF hybrids in CG and CHG contexts compared to no-NBF hybrids when aligned to the almond genome but no difference in methylation levels when aligned to the peach genome. Significantly differentially methylated regions (DMRs) were identified by comparing methylation levels across the genome between NBF- and no-NBF hybrids in each methylation context. In total, 115,635 DMRs were identified based on alignment to the almond reference genome, and 126,800 DMRs were identified based on alignment to the peach reference genome. Nearby genes were identified as associated with the 39 most significant DMRs occurring either in the almond or peach alignments alone or occurring in both the almond and peach alignments. These DMR-associated genes include several uncharacterized proteins and transposable elements. Quantitative PCR was also performed to analyze the gene expression patterns of these identified gene targets to determine patterns of differential expression associated with differential DNA methylation. These DMR-associated genes, particularly those showing corresponding patterns of differential gene expression, represent key targets for almond breeding for future cultivars and mitigating the effects of NBF-exhibition in currently affected cultivars.

Improving genomic predictions with inbreeding and nonadditive effects in two admixed maize hybrid populations in single and multienvironment contexts.

Genetic admixture, resulting from the recombination between structural groups, is frequently encountered in breeding populations. In hybrid breeding, crossing admixed lines can generate substantial nonadditive genetic variance and contrasted levels of inbreeding which can impact trait variation. This study aimed at testing recent methodological developments for the modeling of inbreeding and nonadditive effects in order to increase prediction accuracy in admixed populations. Using two maize (Zea mays L.) populations of hybrids admixed between dent and flint heterotic groups, we compared a suite of five genomic prediction models incorporating (or not) parameters accounting for inbreeding and nonadditive effects with the natural and orthogonal interaction approach in single and multienvironment contexts. In both populations, variance decompositions showed the strong impact of inbreeding on plant yield, height, and flowering time which was supported by the superiority of prediction models incorporating this effect (+0.038 in predictive ability for mean yield). In most cases dominance variance was reduced when inbreeding was accounted for. The model including additivity, dominance, epistasis, and inbreeding effects appeared to be the most robust for prediction across traits and populations (+0.054 in predictive ability for mean yield). In a multienvironment context, we found that the inclusion of nonadditive and inbreeding effects was advantageous when predicting hybrids not yet observed in any environment. Overall, comparing variance decompositions was helpful to guide model selection for genomic prediction. Finally, we recommend the use of models including inbreeding and nonadditive parameters following the natural and orthogonal interaction approach to increase prediction accuracy in admixed populations.

The Reproductive Success of Triturus ivanbureschi × T. macedonicus F1 Hybrid Females (Amphibia: Salamandridae).

Simple SummaryTwo moderately related large-bodied newt species endemic to the Balkan Peninsula, the Balkan crested newt (Triturus ivanbureschi) and the Macedonian crested newt (T. macedonicus), coexist and hybridize in central Serbia. Many generations of mutual hybrid crossings and backcrossings with parental species shaped the genetic composition of hybrid populations. Natural populations have admixed nuclear DNA (nuDNA) of parental species and T. ivanbureschi mitochondrial DNA (mtDNA), which is usually maternally inherited. The mechanisms that direct gene flow and shape the first generations of hybrids could explain the formation of hybrid zones and their maintenance in nature. We followed and compared life history traits related to reproduction of the first generation of reciprocal hybrids obtained by experimental crossing. Our results suggested that possible incompatibilities between mitochondrial and nuclear genomes, which could lead to the exclusion of T. macedonicus mtDNA in natural populations, most likely act at later stages of development or subsequent hybrid generations. Results from this study add to the growing knowledge of Triturus hybrid biology and ecology, which is the baseline for conservation programs necessary to protect these highly endangered amphibians.Two large-bodied newt species, Triturus ivanbureschi and T. macedonicus, hybridize in nature across the Balkan Peninsula. Consequences of hybridization upon secondary contact of two species include species displacement and asymmetrical introgression of T. ivanbureschi mtDNA. We set an experimental reciprocal cross of parental species and obtained two genotypes of F1 hybrids (with T. ivanbureschi or T. macedonicus mtDNA). When hybrids attained sexual maturity, they were engaged in mutual crossings and backcrossing with parental species. We followed reproductive traits over two successive years. Our main aim was to explore the reproductive success of F1 females carrying different parental mtDNA. Additionally, we tested for differences in reproductive success within female genotypes depending on the crossing with various male genotypes (hybrids or parental species). Both female genotypes had similar oviposition periods, number of laid eggs and hatched larvae but different body and egg sizes. Overall reproductive success (percentage of egg-laying females and viability of embryos) was similar for both genotypes. The type of crossing led to some differences in reproductive success within female genotypes. The obtained results suggest that processes that led to exclusion of T. macedonicus mtDNA in natural populations may be related to the survival at postembryonic stages of F2 generation or reproductive barriers that emerged in subsequent hybrid generations.

Житняк — ценная кормовая культура для условий степной зоны Центрально-Черноземного региона

Among bluegrass perennial grasses, wheatgrass are one of the most valuable species for the steppe zone. The wheatgrass (Agropyron pectiniforme Roem. et Shult.) in the herbage of many zones occupy one of the leading positions. This is the most common species among wheatgrass in the wild. At the Voronezh Experimental Station for perennial grasses, primary seed production of the Pavlovsky 12 variety is carried out, based on collected wild-growing samples. Wheatgrass variety Pavlovsky 12 withstands grazing well, and is also well eaten by all farm animals in the hay and pasture. It is the main component of grass mix-tures (wheatgrass + alfalfa or sainfoin) in field and grassland crop rotations. An important condition for increasing the productivity of forage crops is the use of zoned breeding varieties adapted to the specific natural and climatic conditions of cultivation, in this regard, a research program has been developed at the station, which includes wheatgrass in the breeding process, as a more drought-resistant species of peren-nial grasses. In 2011, in order to accomplish the assigned tasks, they began to study the wheatgrass. After 4 years of study, a complex hybrid population of wheatgrass called SGP-8 was formed. In 2015, a com-petitive variety testing of samples with increased forage and seed productivity, drought resistance and resistance to stressful effects of abiotic and biotic environmental factors was started. Based on the results of the research, a promising sample variety was identified, which in 2020 was transferred to the State Commission of the Russian Federation for registration by expert assessment in the State Register of Breeding Achievements Permitted for Use.

Genome-wide insights into adaptive hybridisation across the Schistosoma haematobium group in West and Central Africa.

Schistosomiasis remains a public health concern across sub-Saharan Africa; current control programmes rely on accurate mapping and high mass drug administration (MDA) coverage to attempt disease elimination. Inter-species hybridisation can occur between certain species, changing epidemiological dynamics within endemic regions, which has the potential to confound control interventions. The impact of hybridisation on disease dynamics is well illustrated in areas of Cameroon where urogenital schistosomiasis, primarily due to Schistosoma haematobium and hybrid infections, now predominate over intestinal schistosomiasis caused by Schistosoma guineensis. Genetic markers have shown the ability to identify hybrids, however the underlying genomic architecture of divergence and introgression between these species has yet to be established. In this study, restriction site associated DNA sequencing (RADseq) was used on archived adult worms initially identified as; Schistosoma bovis (n = 4), S. haematobium (n = 9), S. guineensis (n = 3) and S. guineensis x S. haematobium hybrids (n = 4) from Mali, Senegal, Niger, São Tomé and Cameroon. Genome-wide evidence supports the existence of S. guineensis and S. haematobium hybrid populations across Cameroon. The hybridisation of S. guineensis x S. haematobium has not been demonstrated on the island of São Tomé, where all samples showed no introgression with S. haematobium. Additionally, all S. haematobium isolates from Nigeria, Mali and Cameroon indicated signatures of genomic introgression from S. bovis. Adaptive loci across the S. haematobium group showed that voltage-gated calcium ion channels (Cav) could play a key role in the ability to increase the survivability of species, particularly in host systems. Where admixture has occurred between S. guineensis and S. haematobium, the excess introgressive influx of tegumental (outer helminth body) and antigenic genes from S. haematobium has increased the adaptive response in hybrids, leading to increased hybrid population fitness and viability.

Predictability and parallelism in the contemporary evolution of hybrid genomes.

Hybridization between species is widespread across the tree of life. As a result, many species, including our own, harbor regions of their genome derived from hybridization. Despite the recognition that this process is widespread, we understand little about how the genome stabilizes following hybridization, and whether the mechanisms driving this stabilization tend to be shared across species. Here, we dissect the drivers of variation in local ancestry across the genome in replicated hybridization events between two species pairs of swordtail fish: Xiphophorus birchmanni × X. cortezi and X. birchmanni × X. malinche. We find unexpectedly high levels of repeatability in local ancestry across the two types of hybrid populations. This repeatability is attributable in part to the fact that the recombination landscape and locations of functionally important elements play a major role in driving variation in local ancestry in both types of hybrid populations. Beyond these broad scale patterns, we identify dozens of regions of the genome where minor parent ancestry is unusually low or high across species pairs. Analysis of these regions points to shared sites under selection across species pairs, and in some cases, shared mechanisms of selection. We show that one such region is a previously unknown hybrid incompatibility that is shared across X. birchmanni × X. cortezi and X. birchmanni × X. malinche hybrid populations.

Quantitative Trait Loci for Resistance to Potato Dry Rot Caused by Fusarium sambucinum

Tuber dry rot is an important disease of potato caused by soil and seed-borne pathogens of the Fusarium genus leading to losses that may reach 60% of the yield. The goal of this work was to study the inheritance of the dry rot resistance in two diploid potato hybrid populations (11–36 and 12–3) with complex pedigrees, including several wild Solanum spp. We used an aggressive isolate of F. sambucinum for phenotyping both progenies, parents, and standard potato cultivars in laboratory tuber tests, in three subsequent years. The QTL for dry rot resistance were mapped by interval mapping on existing genetic maps of both mapping populations. The most important and reproducible QTL for this trait was mapped on chromosome I and additional year- and population-specific QTL were mapped on chromosomes II, VII, IX, XI, and XII, confirming polygenic control of this resistance. This is the first study mapping the loci affecting tuber dry rot resistance in potato genome that can contribute to better understanding of potato-F. sambucinum interaction and to more efficient breeding of resistant potato cultivars.

Toward Tumor Fight and Tumor Microenvironment Remodeling: PBA Induces Cell Cycle Arrest and Reduces Tumor Hybrid Cells’ Pluripotency in Bladder Cancer

Simple SummaryBladder cancer (BC) is the second most frequent cancer of the genitourinary system. More than 500,000 patients per year are diagnosed with BC, a disease which additionally results in more than 200,000 annual deaths. One of the major problems in BC treatment is that many patients cannot receive appropriate treatment due to comorbidities and the severe inflammatory side effects of therapy. The aim of our study was to assess the effect of butyrate derivatives, demonstrating that they could be beneficial for treating the tumor and also to modify the tumor microenvironment. Upon treatment with butyrate derivatives, we particularly saw increased PD-L1 surface expression and reduced pluripotency molecular markers in a hybrid BC–macrophage cell population. This is a cell population known to display an increased capacity to migrate and evade immunity. Treatment with butyrate derivatives may also provide a better chance of immunotherapy success for BC patients.Bladder cancer (BC) is the second most frequent cancer of the genitourinary system. The most successful therapy since the 1970s has consisted of intravesical instillations of Bacillus Calmette–Guérin (BCG) in which the tumor microenvironment (TME), including macrophages, plays an important role. However, some patients cannot be treated with this therapy due to comorbidities and severe inflammatory side effects. The overexpression of histone deacetylases (HDACs) in BC has been correlated with macrophage polarization together with higher tumor grades and poor prognosis. Herein we demonstrated that phenylbutyrate acid (PBA), a HDAC inhibitor, acts as an antitumoral compound and immunomodulator. In BC cell lines, PBA induced significant cell cycle arrest in G1, reduced stemness markers and increased PD-L1 expression with a corresponding reduction in histone 3 and 4 acetylation patterns. Concerning its role as an immunomodulator, we found that PBA reduced macrophage IL-6 and IL-10 production as well as CD14 downregulation and the upregulation of both PD-L1 and IL-1β. Along this line, PBA showed a reduction in IL-4-induced M2 polarization in human macrophages. In co-cultures of BC cell lines with human macrophages, a double-positive myeloid–tumoral hybrid population (CD11b+EPCAM+) was detected after 48 h, which indicates BC cell–macrophage fusions known as tumor hybrid cells (THC). These THC were characterized by high PD-L1 and stemness markers (SOX2, NANOG, miR-302) as compared with non-fused (CD11b−EPCAM+) cancer cells. Eventually, PBA reduced stemness markers along with BMP4 and IL-10. Our data indicate that PBA could have beneficial properties for BC management, affecting not only tumor cells but also the TME.