Favorable Genotype Research Articles

An Investigation of Polymorphism on the FASN, SCD1, and SLC27A3 Genes in Sheep

Milk traits of sheep are affected by many environmental and genetic factors. These traits are quantitative traits and are determined by many genes. This study aimed to investigate polymorphisms of milk-related Fatty-acid synthase (FASN), Stearoyl-CoA desaturase (SCD1), and solute carrier 27A3 (SLC27A3) genes in cross-bred Hamdani sheep. Blood samples were collected from 100 healthy cross-bred Hamdani ewes from the jugular vein into K3-EDTA-containing tubes. Genomic DNA was extracted using a commercial DNA isolation kit. PCR products of FASN (275 bp), SCD1 (225 bp), SLC27A3-P1 (341 bp), and SLC27A3-P2 (319 bp) were subjected to restriction fragment length polymorphism (RFLP) analysis using SSil (AciI), Cfr13I, AluI, and Hpy188III the restriction enzyme, respectively. However, all gene regions were found to be monomorphic. In the study, only TT, AA, AA, and GG genotypes were detected for FASN, SCD1, SLC27A3-P1, and SLC27A3-P2, respectively. Allele and genotype frequencies were 1.00 for all genotypes and alleles. Although this study did not reveal favorable genotypes in FASN, SCD1, and SLC27A3 genes that can be used for milk traits, more comprehensive studies with larger sample sizes should be conducted to investigate polymorphisms in cross-bred Hamdani sheep.

Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America

Cassava (Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa is severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play a pivotal role in preserving crop diversity, providing crucial resources for breeding resilient and disease-resistant crops. This study genotyped 234 South American cassava accessions conserved at the CIAT genebank, previously phenotyped for CBSD resistance by an independent group, to perform a genome-wide association analysis (GWAS) to identify genetic variants associated with CBSD resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, associated with disease severity or the presence/absence of viral infection. Markers were annotated within or near genes previously identified with functions related to pathogen recognition and immune response activation. Using the SNP candidates, we screened the world’s largest cassava collection for accessions with a higher frequency of favorable genotypes, proposing 35 accessions with potential resistance to CBSD. Our results provide insights into the genetics of CBSD resistance and highlight the importance of genetic resources to equip breeders with the raw materials needed to develop new crop varieties resistant to pests and diseases.

Identification of single nucleotide polymorphisms in BMP-2 gene and their associations with productive traits in Rainbow Trout

Relevance. Aquaculture is occupying an increasingly important place in fish farming, as it allows obtaining more products per unit area. In recent years, special attention has been paid to the development of new breeds of Rainbow Trout in order to obtain fish forms adapted to aquaculture conditions. One of the significant breeding achievements is the Ropshinsky golden trout, characterized by attractive scale coloration. Taking into account the emergence of such forms of fish, research to identify genetic characteristics is of particular relevance. The BMP-2 gene is an important determinant of fish growth and development, so a comprehensive study of its structure will allow us to identify the most favorable genotypes in producers for their use in further selection and breeding.Results. The aim of the work is to identify single nucleotide polymorphisms (SNPs) in the studied gene and link their presence in parental forms with their productive traits. In particular, after sequencing, several SNPs were identified in different positions both in the intron and exon regions of the gene. The frequencies of occurrence of genotypes in parents were calculated and a number of quantitative traits were measured in the offspring numbered of 50 individuals from each crossing pair. In some cases, it was possible to establish statistically significant associations between the identified SNPs and productive traits in females and males — the parents of the resulting offspring. In females, an association was established between head length and SNP in one gene region, and in males, an association of another polymorphism with ejaculate volume has been demonstrated.

Genotyping of Holstein Cows by SELL, MX1 and CXCR1 Gene Loci Associated With Mastitis Resistance.

Mastitis is a significant factor that decreases milk production in cows of different breeds in Kazakhstan. The objective of this study was to determine the genetic makeup of Holstein cows by analysing specific gene loci (SELL, MX1, CXCR1+291C>T and CXCR1+1093C>T) that are linked to resistance against mastitis. The goal was to identify cows with favourable genotypes that are less prone to udder diseases. At the SELL gene locus c.567T>C, all three genetic variants were identified in the control population with the respective frequencies: TT (0.20), CT (0.44), and CC (0.36). Genetic variation was also detected at the MX1 gene c.567T>C, CXCR1 c.+291C>T and CXCR1+1093C>T loci. Deviation from the expected Hardy-Weinberg equilibrium was observed for two gene loci, MX1 g.143182088 and CXCR1+1093C>T, with increased chi-square values of 10.6261 and 9.7137, respectively. The analysis of subclinical mastitis incidence indicates that cows carrying the heterozygous CT genotype at the L-selectin gene locus exhibit greater resistance to the disease. Animals carrying the CCCCCT genotype at the MX1 c.567T>C, CXCR1 c.+291C>T and CXCR1+1093C>T gene loci were discovered to have a significant likelihood of developing subclinical mastitis. This suggests that these genes could serve as potential indicators of susceptibility to the condition. The practical significance of this study lies in determining the frequency of genotypes linked to mammary gland morbidity in Holstein breeding farms in Kazakhstan.

Association of Genetic Profile with Muscle Mass Gain and Muscle Injury Prevention in Professional Football Players after Creatine Supplementation.

In recent years, the study of creatine supplementation in professional athletes has been of great interest. However, the genetics involved in response to supplementation is unknown. The aim of this study was to analyse, for the first time, the relationship between muscle performance-related genes and the risk of an increased body mass index (BMI) and muscle mass and a decrease in fat mass in professional football players after creatine supplementation. For this longitudinal study, one hundred and sixty-one men's professional football players were recruited. The polymorphisms ACE I/D, ACTN3 c.1729C>T, AMPD1 c.34C>T, CKM c.*800A>G, and MLCK (c.49C>T and c.37885C>A) were genotyped using Single-Nucleotide Primer Extension (SNPE). To assess the combined impact of these six polymorphisms, a total genotype score (TGS) was calculated. The creatine supplementation protocol consisted of 20 g/day of creatine monohydrate for 5 days (loading dose) and 3-5 g/day for 7 weeks (maintenance dose). Anthropometric characteristics (body mass index (BMI), fat, and muscle mass) were recorded before and after the creatine supplementation protocol. Characteristics of non-contact muscle injuries during the 2022/2023 season were classified according to a consensus statement for injury recording. The results showed that the allelic frequencies of ACE and AMPD1 differed between responders and non-responders in muscle mass increase (all p < 0.05). Players with a TGS exceeding 54.16 a.u. had an odds ratio (OR) of 2.985 (95%CI: 1.560-5.711; p = 0.001) for muscle mass increase. By contrast, those with a TGS below 54.16 a.u. had an OR of 9.385 (95%CI: 4.535-19.425; p < 0.001) for suffering non-contact muscle injuries during the season. The increase in BMI and muscle mass in response to creatine supplementation in professional football players was influenced by a TGS derived from the combination of favourable genotypes linked to muscle performance. The CC genotype and C allele of AMPD1 were particularly associated with a higher likelihood of muscle mass increase under creatine supplementation in this group of professional football players.

A genome-wide association study reveals novel loci and candidate genes associated with plant height variation in Medicago sativa

BackgroundPlant height (PH) is an important agronomic trait influenced by a complex genetic network. However, the genetic basis for the variation in PH in Medicago sativa remains largely unknown. In this study, a comprehensive genome-wide association analysis was performed to identify genomic regions associated with PH using a diverse panel of 220 accessions of M. sativa worldwide.ResultsOur study identified eight novel single nucleotide polymorphisms (SNPs) significantly associated with PH evaluated in five environments, explaining 8.59–12.27% of the phenotypic variance. Among these SNPs, the favorable genotype of chr6__31716285 had a low frequency of 16.4%. Msa0882400, located proximal to this SNP, was annotated as phosphate transporter 3;1, and its role in regulating alfalfa PH was supported by transcriptome and candidate gene association analysis. In addition, 21 candidate genes were annotated within the associated regions that are involved in various biological processes related to plant growth and development.ConclusionsOur findings provide new molecular markers for marker-assisted selection in M. sativa breeding programs. Furthermore, this study enhances our understanding of the underlying genetic and molecular mechanisms governing PH variations in M. sativa.

Genome-Wide Association Study for Maize Hybrid Performance in a Typical Breeder Population.

Maize is one of the major crops that has demonstrated success in the utilization of heterosis. Developing high-yield hybrids is a crucial part of plant breeding to secure global food demand. In this study, we conducted a genome-wide association study (GWAS) for 10 agronomic traits using a typical breeder population comprised 442 single-cross hybrids by evaluating additive, dominance, and epistatic effects. A total of 49 significant single nucleotide polymorphisms (SNPs) and 69 significant pairs of epistasis were identified, explaining 26.2% to 64.3% of the phenotypic variation across the 10 traits. The enrichment of favorable genotypes is significantly correlated to the corresponding phenotype. In the confident region of the associated site, 532 protein-coding genes were discovered. Among these genes, the Zm00001d044211 candidate gene was found to negatively regulate starch synthesis and potentially impact yield. This typical breeding population provided a valuable resource for dissecting the genetic architecture of yield-related traits. We proposed a novel mating strategy to increase the GWAS efficiency without utilizing more resources. Finally, we analyzed the enrichment of favorable alleles in the Shaan A and Shaan B groups, as well as in each inbred line. Our breeding practice led to consistent results. Not only does this study demonstrate the feasibility of GWAS in F1 hybrid populations, it also provides a valuable basis for further molecular biology and breeding research.

Stability analysis of spring oat genotypes in south-west Poland

Summary Oat is a grain in high demand, due to its physiological and nutritional attributes as a functional food. Oat is rich in β−glucans, and high in tocopherol and other dietary fibre components. It is also used for forage, fodder, chaff and as a major component of infant foods. In the present study, oat yields from six experimental stations in south-western Poland, obtained in 2019–2022, were analysed using three different linear mixed models that can be associated with three different stabilities. It is shown that the genotype Perun had the highest mean yield among the tested genotypes, while the genotype Armani was the most stable. Armani and Pablo had the lowest values of the GSI index, making them the most favourable genotypes for cultivation in that region.

Genetic analysis of invasive spread of wintercreeper (Euonymus fortunei), a popular ornamental groundcover

AbstractAn important route of introduction of some nonnative species that subsequently become invasive in the United States is through horticulture. One such plant is Euonymus fortunei (Turcz.) Hand.-Maz., commonly known as wintercreeper, an evergreen groundcover with more than 52 different horticultural varieties, which is still sold at many plant nurseries and garden centers in the midwestern United States. Although several states have recognized E. fortunei as an invasive species, it is unknown how its escape from cultivation has occurred and even the identity of spreading populations, including whether hybrids or cultivars are involved. Using codominant microsatellite markers, we sampled multiple invasive populations in Ohio, Kentucky, Kansas, and Minnesota and compared their genotypes with commercially available cultivars to determine how spread has occurred. All samples collected from invasive populations were genetically identical to one another and matched perfectly with the ‘Coloratus’ cultivar, the only cultivar to exhibit polyploidy. The data also suggest that E. fortunei may potentially reproduce via apomixis and/or clonally through propagule fragments, which can quickly fix favorable genotypes within a population. To curb continued invasive spread, we suggest that Coloratus be removed from commercial sale and distribution. We also propose that land managers, horticultural and landscaping businesses, and governmental agencies carefully monitor other Euonymus cultivars for invasive potential and spread.

Polymorphisms within the &lt;em&gt;IGF1&lt;/em&gt; and &lt;em&gt;IGF1R&lt;/em&gt; genes associated with superovulation-related traits in Holstein dairy cows managed in a semiarid environment

Embryo transfer (ET) is an artificial reproductive technology used for the genetic improvement of cattle. High variation has been observed in superovulation (SPO) and embryo flush recovery, which appear to be influenced by donor cow genetics. Then, the objective was to identify single nucleotide polymorphisms (SNPs) from the genes IGF1 and IGF1R associated with reproductive traits related to SPO response in dairy cows raised in a semiarid region. Sixty-four Holstein cows were subjected to SPO, artificial insemination, and nonsurgical embryo collection. Individual blood samples were collected and used to genotype 13 SNPs from the genes IGF1 and IGF1R. Additional blood samples were collected to measure anti-Mullerian hormone (AMH) concentrations. Ovarian and embryo traits related to SPO response were evaluated. A mixed-effects model was used to identify associations between SNPs and SPO-related traits. A regression model was implemented to calculate allele substitution effects. From 13 SNPs, the SNP rs109763947 in the gene IGF1 and the SNPs rs110343126 and rs208140993 in the gene IGF1R were predictors for six traits evaluated in superovulated cows. The most favorable genotypes for these SNPs were CC, AA and GG, respectively. A linear trend was detected, suggesting an additive effect of the genes. Moreover, all traits evaluated in the current study improved as the number of favorable SNP genotypes increased, confirming a positive contribution of the SNP genes. In conclusion, three SNPs in the genes IGF1 and IGF1R were marker predictors for reproductive traits related to SPO response and embryo production in Holstein cows managed in a semiarid region.

Changes in Genotype Composition and Morphology at an Experimental Site of Common Reed (Phragmites australis) Over a Quarter of a Century

The cultivation of common reed (Phragmites australis) is one of the most promising practices of paludiculture on fen peatlands. This highly productive grass has a high adaptation capacity via high levels of genetic diversity and phenotypic plasticity. In this study, a reed experimental site established on a degraded fen in 1996/97 with a mixture of monoclonally (meristematically propagated plantlets) and polyclonally (pre-grown seedlings) planted plots was investigated by microsatellite genotyping. All nine genotypes of the monoclonal planted plots were recovered and could be genetically characterized; invasion by other genotypes was negligible. Similarly, the polyclonal plots sustained high clonal diversity with no prevalence of a single genotype. The growth characteristics of the five quantitatively investigated genotypes significantly differed from each other (α = 0.05): dry biomass per stem 5–18 g, panicles per m2 20–60, average stem diameter 3.5–6 mm, height 170–250 cm. Similarly, the persistence of genotypes at the planted plots and their invasiveness (ability to invade neighboured plots) varied. These results show that common reed stands are extremely persistent even if established with genotypes that are likely not to be locally adapted. Their genetic structure remained stable for at least 24 years regardless of the planting density (1, 4, and 10 plants per m2). Our results indicate that farmers may be able to maintain favourable genotypes for many years, thus the selection and breeding of common reed as a versatile crop for rewetted peatlands is a promising objective for paludiculture research.

Genotype sensitivity and adaptability for fruit yield in red and green okra on environmental change

Abstract. Abdillah SM, Syukur M, Suwarno WB, Ritonga AW, Wahyudi A. 2023. Genotype sensitivity and adaptability for fruit yield in red and green okra on environmental change. Biodiversitas 24: 4289-4298. Okra is vegetable plant consumed in immature and beneficial plants of various health. For breeders, this crop had a big chance to develop a high-yield genotype in various conditions. To develop a new variety must be known adaptability and stability in environment tests. This research aimed to evaluate the fruit yield response, sensitivity, and adaptability of okra genotypes in four environment trials. A randomized complete block design with three replications was used in each environment, with ten okra genotypes as the treatment. The AMMI-1, AMMI-2 and GGE biplot was used to illustrate genotype stability and their adaptability. Genotype by environment interaction significantly affected fruit yield, with the environment having a large contribution, with SWR01 being the highest yield. The rate of rainfall and PC1 were explained as 36.98% and 70.17% to the GEI sum of squares, respectively. ‘ZAHIRA’ and ‘GSO03’ showed sensitivities to the rate of rainfall. Genotypes ‘SWR01’ and ‘GSO03’ were the most favorable genotype according to ASV and yield performance across environments The AMMI-1, AMMI-2 and GGE biplot confirmed that both were the most suitable genotype for developing a recent variety of okra in a wide environment.

GWAS-identified telomere length associated genetic variants predict risk of recurrence of HPV-positive oropharyngeal cancer after definitive radiotherapy.

Lymphocyte telomere length (LTL)-related genetic variants may modulate LTL and affect recurrence of squamous cell carcinoma of the oropharynx (SCCOP). A total of 1013 patients with incident SCCOP were recruited and genotyped for 16 genome-wide association study (GWAS)-identified TL-related polymorphisms. Of these patients, 489 had tumour HPV16 status determination. Univariate and multivariate analyses were performed to evaluate associations. Of the 16TL-related polymorphisms, four were significantly associated with LTL: rs1920116, rs3027234, rs6772228, and rs11125529, and the patients with putatively favourable genotypes had approximately 1.5-3 times the likelihood of shorter LTL compared with patients with the corresponding risk genotypes. Moreover, patients with one to four favourable genotypes of the four combined polymorphisms had approximately 3-11 times the likelihood of shorter LTL compared with patients with no favourable genotype. The four LTL-related polymorphisms were significantly associated with approximately 40% reduced risk (for favourable genotypes) or doubled risk (for risk genotypes) of recurrence, and similar but more pronounced associations were observed in patients with tumour HPV16-positive SCCOP. Similarly, patients with one to four risk genotypes had significantly approximately 2.5-4 times increased recurrence risk compared with patients with no risk genotype, and similar but more pronounced associations were observed in patients with tumour HPV16-positive SCCOP. Four LTL-related polymorphisms individually or jointly modify LTL and risk of recurrence of SCCOP, particularly HPV-positive SCCOP. These LTL-related polymorphisms could have potential to further stratify patients with HPV-positive SCCOP for individualized treatment and better survival. Not applicable.

Polymorphism studies and candidate genes associated with litter size traits in Indonesian goats. a systematic review

Background: Litter size (LS) is a significant, challenging, and economical aspect of the goat industry in Indonesia. It is influenced by several different factors and genes; consequently, identifying potential genes and loci associated with litter size has become a genetic problem. Several genetic indicators have been found to be associated with litter size in goats. This has prompted the need to discuss candidate genes associated with litter size in goats in Indonesia. Methods: A systematic review was conducted using critical databases including ResearchGate, Google Scholar, PubMed, Google search engine and Science direct. There were any exclusion criteria, they were as follows: articles published in languages other than English, Conference papers, short communication papers and papers not related to animals. After reviewing the abstracts of 42 publications, the remaining 17 investigations were chosen for full paper evaluation. A further eight studies were removed after a comprehensive evaluation of the publications because they did not match our inclusion criteria. Results: These markers include growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15), bone morphogenetic protein receptor type IB (BMPR1B), and kisspeptin (KISS1). Single nucleotide polymorphisms in these genes contribute to the development of novel genetic markers that helps in the selection of goats with the most favorable genotypes for litter size. This type of genetic selection is more successful than the traditional way of selecting animals for reproductive traits, particularly litter size. Conclusions: As a result, this study summarizes the genetic impacts of polymorphisms in candidate genes associated with litter size features in Indonesian goats.

Selection of Suitable Genotypes Based on Physiological and Morphological Traits in Rapeseed (Brassica napus L.)

Aims: Rapeseed (Brassica napus L.) as one of the most important oilseeds in the world, has a special role in cultivation and plant breeding research. Especially, the properties of rapeseed oil compounds, which have high oleic acid, antioxidant and positive effects on cholesterol, blood sugar control, blood pressure and cancer, make it one of the healthiest and most important edible oils in the world and an alternative to use Other vegetable oils have been introduced in recent years. Evaluation of different genotypes of Rapeseed in terms of different traits and selection of the most appropriate genotypes can be effective in realizing the goals of plant breeding.&#x0D; Study Design: In order to conduct the experiment, a randomized complete block design (RCBD) was used in three replications.&#x0D; Place and Duration of Study: This study was conducted in Varamin region of Iran in 2019-2020.&#x0D; Methodology: Each experimental plot had 4 rows of cultivation at a distance of 50 cm. The seeds were planted at a distance of 10 cm from each other and all steps such as watering and weeding were done regularly and manually.&#x0D; Results: The results of analysis of variance at the level of 0.01 indicated that the evaluated genotypes have significant differences in terms of all traits except the number of grains in the pod. In the means comparison of the traits, grain yield and oil percentage traits, which were selected as the most important traits, the Licord genotype was selected as the most favorable genotype. Based on the correlation analysis between the traits, the trait of grain yield had a positive and significant correlation with the traits of thousand grain weight, number of pods in the main stem, pod weight, days to flowering and oil percentage. Based on analysis of the main components, the first five components accounted for more than 74% of the variance of the total data. The drawn polygon diagram also identified Licord, Hyola-401, SLM046, Modena and Option 500 genotypes as desirable genotypes.&#x0D; Conclusion: Non-invasive independent predictors for screening esophageal varices may decrease medical as well as financial burden, hence improving the management of cirrhotic patients. These predictors, however, need further work to validate reliability.

IFNL4 Genotype Frequencies in Asian Populations Support Shorter Duration Therapy with Sofosbuvir-Based Hepatitis C Virus Regimens to Increase the Number Cured.

Globally, ∼56.8 million people are chronically infected with hepatitis C virus (HCV), with about half residing in Asia. The cost and efficiency of delivering regimens based on direct-acting antiviral agents for HCV are important considerations in implementing these curative treatments. For sofosbuvir-based regimens, most patients are treated for 12 weeks; however, treatment for 8 weeks has been shown to cure HCV infection in 95% of patients without cirrhosis. Furthermore, virological failure after 8-week treatment occurs in only 1%-2% of individuals without cirrhosis, who have a favorable IFNL4 genotype, which is present in >50% of South Asians and >80% of East Asians. We propose that sofosbuvir-based treatment for 8 weeks, or perhaps shorter, would yield high response rate regimens in Asian countries and markedly increase the number of patients who could be cured for a given cost of the medication. We propose that a noninferiority trial in an East Asian population be conducted to test this hypothesis.

P-498 Towards precision medicine: maternal genetic profiles as determinant of adequate decidualization and reproductive success; a prospective study in oocyte donation cycles.

Abstract Study question To determine the impact of genes related to decidualization and immune cell activation as predictors for reproductive success. Summary answer Women with unfavorable genetic profiles for Human Leukocyte Antigen (HLA)-F and Killer Immunoglobulin-like Receptor (KIR) genes showed decreased pregnancy rates. What is known already KIR genes encode receptors present on uterine Natural Killer (uNK) cells that are essential during placentation and early gestation. It has been established that women of KIR AA genotype show lower reproductive success than KIR BX, due to the lack of activation of these immune cells. Additionally, another gene, HLA-F, expressed in endometrial cells, also seems to be involved in the recruitment and supplementary activation of uNKs. Certain alleles of this gene appear to decrease its expression in the uterus and hinder the processes in which it is involved during the decidualization process, decreasing implantation rates and increasing time-to-pregnancy. Study design, size, duration We conducted a prospective cohort study with 75 patients, with no history of recurrent miscarriage or implantation failure, who attended our institution to undergo assisted reproduction treatments (ART) with donated oocytes, between January 2021 and December 2022. By using the egg donation model, we were able to investigate the endometrial cell population avoiding the oocyte factor bias Participants/materials, setting, methods All patients included were under 45 years of age (40.5 ± 2.9 years), had a normal BMI (21.6 ± 1.9 kg/m2) and had not been diagnosed with uterine pathologies or immunological conditions. All recipients were genotyped for the KIR and HLA-F genes and pregnancy, miscarriage (MR) and live birth rates (LBR) obtained in their egg donation cycles were recorded. Fisher's test was used to determine statistically significant differences (p &amp;lt; 0.05) between groups Main results and the role of chance Patients were divided into two groups according to their KIR genotype: 29 KIR AA (inhibitor) and 46 KIR BX (activator). In each group, allelic load was determined for the three HLA-F regions studied (RS1362126, RS2523405 and RS2523393). For all these regions, patients with favorable HLA-F alleles and KIR BX genotype had higher pregnancy rates than KIR AA patients with unfavorable HLA-F alleles (85.42 % vs 54.17% for RS1362126 region, OR = 4.956, p = 0.008; 83.33% vs 58.62% for RS2523405 region, OR = 3.529, p = 0.0295; 82.5% vs 57.69% for RS2523393 region, OR = 3.457, p = 0.0462). No significant differences were obtained for MR or LBR. This demonstrates the involvement of KIR and HLA-F in embryo implantation and that the coincidence of unfavorable alleles for both decreases reproductive success considerably, probably due to impaired decidualization and lack of uNK recruitment and activation. No significant differences were obtained for the rest of the genetic profiles, except when comparing pregnancy rate of KIR AA women with favorable HLA-F alleles to KIR AA women with unfavorable HLA-F alleles for the RS1362126 region (79.41% vs 54.17%, OR = 3.264, p = 0.04). The latter finding suggests that the lack of uNK cell activation, so evident in KIR AA patients, could be compensated by expressing favorable HLA-F alleles. Limitations, reasons for caution The low sample size of this study does not allow us to compare groups taking into account other genes, such as embryonic HLA-C, which also, and in combination with KIR genotypes, has been shown to play a role in proper implantation and placentation. Wider implications of the findings uNKs activation is required to promote embryo implantation. Combination of unfavorable genetic profiles involved in these immune mechanism leads to lower pregnancy rate. The study of these genetic profiles can help to predict reproductive success, thus identifying patients susceptible to receive immunological treatment before embryo transfer, possibly decreasing their time-to-pregnancy. Trial registration number Not applicable

Maintenance and expansion of genetic and trait variation following domestication in a clonal crop.

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterize the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and a principal starch staple for 20 million Ethiopians. Wild enset reproduction occurs strictly by sexual outcrossing, but for cultivation, it is propagated clonally and associated with diversification and specialization into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested an accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by the amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages, we found a significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. The development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.

Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches.

'Chinese Cling' is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145 456 single-nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solids content, along with 14 key volatile odor compounds (VOCs), were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified as associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solids content, and cis-3-hexenyl acetate. Multiple-trait genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-trait model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in the 'Shanghai Shuimi' landrace. Overall, our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars.

Non-parametric Measures for Yield Stability in Faba Bean (Vicia faba L.) Advanced Line in Gangetic Plains of India

Background: Multi environmental trials (MET) is central activity in crop improvement programs for identification of superior genotype across environment before release as a variety. The aim of the present study was to select faba bean genotypes having high seed yield and most stable performance across different environments in gangetic plains of India. Methods: The material for the study consisted of set of 11 genotype of faba bean subjected to multi-locational seed yield trials for three years (2015-2018) at four locations. The test of significance for genotype x environment (GE) interaction and eight non-parametric measures of stability analysis were used to identify high yield stable genotype across the five environments. A new approach Combined Stability Index based on yield stability performance calculated based on the ranking of the used stability measures of all the genotypes. Result: Based on low value of Combined Stability Index, HB-12-37, (CSI(i) = 10) HB-11-15, (CSI(i) = 11), HB-11-32 (CSI(i) = 14) were identified as the most stable genotypes with high yield potential. These non-parametric measures were observed to be associated with high mean seed yield. The simple rank correlation coefficient, calculated using the ranks was used to measure the association among the eight stability statistics and mean seed yield. The nature of relationships among the non-parametric measures was assessed and these stability measures are categorized in three groups. The genotype HB-12-37 (G3) fall in section 1 were the most favourable genotype due to high seed yield as well as high stability performance according to plot of all non-parametric measures with seed yield. HB-12-37 (G3) which had higher seed yield (25.19 q / ha) and high protein content (24.85%) with better stability across the environments could be used in further breeding programmes of faba bean and recommended for release as variety for plains of India.