Significant Genotype Research Articles

Nutritional Potential of Adzuki Bean Germplasm and Mining Nutri-Dense Accessions through Multivariate Analysis.

The adzuki bean (Vigna angularis), known for its rich nutritional composition, holds significant promise in addressing food and nutritional security, particularly for low socioeconomic classes and the predominantly vegetarian and vegan populations worldwide. In this study, we assessed a total of 100 diverse adzuki bean accessions, analyzing essential nutritional compounds using AOAC's official analysis procedures and other widely accepted standard techniques. Our analysis of variance revealed significant genotype variations for all the traits studied. The variability range among different traits was as follows: moisture: 7.5-13.3 g/100 g, ash: 1.8-4.2 g/100 g, protein: 18.0-23.9 g/100 g, starch: 31.0-43.9 g/100 g, total soluble sugar: 3.0-8.2 g/100 g, phytic acid: 0.65-1.43 g/100 g, phenol: 0.01-0.59 g/100 g, antioxidant: 11.4-19.7 mg/100 g GAE. Noteworthy accessions included IC341955 and EC15256, exhibiting very high protein content, while IC341957 and IC341955 showed increased antioxidant activity. To understand intertrait relationships, we computed correlation coefficients between the traits. Principal Component Analysis (PCA) revealed that the first four principal components contributed to 63.6% of the variation. Further, hierarchical cluster analysis (HCA) identified nutri-dense accessions, such as IC360533, characterized by high ash (>4.2 g/100 g) and protein (>23.4 g/100 g) content and low phytic acid (0.652 g/100 g). These promising compositions provide practical support for the development of high-value food and feed varieties using effective breeding strategies, ultimately contributing to improved global food security.

Genotype by environment interaction for agro-morphological traits and herbage nutritive values and fodder yield stability in oat (Avena sativa L.) using AMMI analysis in Ethiopia

This study aimed to evaluate the genotype by environment interaction for agro-morphological traits and fodder nutritive values of oat (Avena sativa L.) genotypes under diverse environmental conditions and to identify high fodder yielding and consistently performing genotypes in Ethiopia. Oat genotypes usually demonstrate inconsistent performance in different environments due to variations in growing environments and the existence of significant genotype by environment interaction complicates the selection process. Therefore, the genotype by environment interaction study was executed using the additive main effects and multiplicative interactions model to select superior and stable genotypes. The effects of genotype by environment interaction on fodder yield stability in twenty-four oat genotypes were investigated in nine environments using a randomized complete block design. The additive main effects and multiplicative interaction analysis of variance for fodder yield showed significant variation for genotype, environment, and genotype by environment interaction effects and the highest contributor for the total variation was the environment (67.45 %) main effect followed by genotype by environment interaction (22.73 %) and the genotype (9.82 %). The first (44.11 %) and the second (26.79 %) interaction principal component axes were significant and cumulatively accounted for 70.91 % of the total interaction variance. Based on the first two additive main effects and multiplicative interaction analyses, E6, E4, and E2 were located far from the biplot origin and had a high contribution to the total variation of genotype by environment interaction. The fodder yield of the genotypes G6, G10, G23, G7, G9, G18, G13, G1, G24, G15, G2, G3, G19, G4, and G11 were above the grand mean. The fodder yield stability result obtained from the second additive main effects and multiplicative interaction is usually more accurate compared to the first additive main effects and multiplicative interaction. Consequently, genotypes which had mean fodder yield above the grand mean and relatively stable performance were observed for G23, G6, G10, G7, G11, G1, G9, G15, G2, G3, G4, and G19. However, G2, G3, G4, G11, and G19 have released varieties while the remaining genotypes have not been yet released. Therefore, G6, G10, G23, G7, and G9 were selected for verification and cultivation of these selected genotypes would contribute more for oat fodder yield improvement programs in Ethiopia.

Comparative study of univariate and multivariate selection strategies based on an integrated approach applied to oilseed rape breeding

AbstractChoosing the right method to discover superior genotypes is always one of the major challenges that oilseed rape (Brassica napus L.) researchers deal with. This work aimed to compare the univariate and multivariate selection indices utilizing variance‐based, additive main effects and multiplicative interaction based, best linear unbiased prediction based, and genotype × environment/trait based strategies to determine the best‐performing (regarding stability, yield, and agronomic traits) oilseed rape genotypes. Utilized indices were categorized into five general methods, including univariate performance selection index (UPSI: mean performance), univariate stability selection indices (USSIs: environmental variance, Shukla's stability variance, AMMI stability value, modified AMMI stability value, modified AMMI stability index, and weighted average of absolute scores), multivariate performance selection indices (MPSIs: genotype by trait [GT], genotype by yield × trait [GYT], and ideotype‐design index [FAI‐BLUP]), univariate performance and stability selection indices (UPSSIs: coefficient of variability, harmonic mean of genotypic value [HMGV], relative performance of genotypic value [RPGV], WAASBY [WAASB and mean performance {Y}], and genotype + genotype × environment interaction [GGE]), and multivariate performance and stability selection index (MPSSI: MTSI). Data from 18 oilseed rape genotypes and two checks were obtained from trials conducted at eight locations in Iran during two consecutive crop years from 2018 to 2020. The grain yield (GY) and agronomic traits were evaluated. The significant genotype × environment interaction was found for GY and agronomic traits in the combined analysis of variance. In terms of GY, the selection indices GGE, HMGV, and RPGV (6.51), GYT (6.43), GT (5.35), MTSI (4.95), FAI‐BLUP (4.64), and WAASBY (3.97) achieved better‐than‐average genetic gains (GSs). Using an optimized model of USSIs (O‐USSIs), GS increased from −0.15 to 3.26 on average, which shows the efficiency of O‐USSIs in high‐yielding and stable genotypes selection. Based on Spearman's ranking correlation, a positive relationship was found among MPSIs, MPSSI, UPSSIs, and UPSIs, but not for USSIs. Based on an integrated model of selection indices, genotypes G2, G10, G11, G14, and G20 were detected as superior genotypes with high‐yielding, high‐stability, and desirable agronomic traits. It could be concluded that combining different approaches of genotype selection based on an integrated model can provide better answers to oilseed rape breeders.

28 Social Support, APOE Genotype, and Memory Associations in a Community-Based Sample of Older Adults in Texas

Objective:The apolipoprotein E (APOE) gene has been identified as a major risk factor for the development of Alzheimer’s disease in late life. Research has shown that APOE e4 allele carriers demonstrate poorer memory performance and accelerated cognitive decline relative to non-carriers, and there is a need to identify potential factors of resiliency against the negative effects of e4 on cognition. Social support may represent one potential mechanism given that higher levels of social support have been linked to better cognitive and functional outcomes in older adults. Thus, the current study sought to examine whether social support moderates the relationship between APOE e4 status and subjective and objective memory performance in a large community-based sample of Hispanic/Latino (H/L) and Non-Hispanic White (NHW) older adults residing in Texas.Participants and Methods:Participants included 1,564 (H/L = 808, NHW = 756) older adults (mean age = 66.36±8.68) without dementia that had enrolled in the Health and Aging Brain Study-Health Disparities. Participants completed study questionnaires and a comprehensive neuropsychological battery. Apolipoprotein e4 status (e4 carriers vs. non-carriers) was determined by possession of at least one e4 allele. Perceived social support was measured using the total score from the abbreviated 12-item version of the Interpersonal Support Evaluation List. Objective memory performance was assessed using a z-score composite of Story A and B from the Weschler Memory Scale (WMS)-III and immediate and delayed recall trials from the Spanish-English Verbal Learning Test. Subjective memory was assessed using the total score from the Subject Memory Complaints Questionnaire. Race stratified multiple linear regression models, controlling for age, sex, and years of education, examined APOE e4 positivity x social support interactions on subjective and objective memory performance.Results:There was a significant APOE e4 genotype x social support interaction on objective memory performance (ß = -1.10, p = 0.003) in H/Ls such that higher levels of social support were associated with better memory performance in non-e4 carriers (ß = 0.14, p < .001), but not in e4 carriers (ß = -0.13, p = 0.9). In contrast, no significant APOE e4 status x social support interaction was observed on subjective memory (ß = -0.39, p = 0.35) in H/Ls. Finally, results revealed no significant APOE e4 genotype x social support interactions on subjective memory (ß = 0.14 p = 0.77) or objective memory (ß = 0.67, p = 0.11) performance in NHWs. Conclusions: Findings revealed that social support did not mitigate against the negative effects of e4 on subjective and objective memory performance in H/Ls or NHWs. However, results demonstrate that higher levels of social support are associated with better objective, but not subjective memory performance in H/Ls without the e4 genotype. These findings suggest that social support may protect against cognitive decline and enhance cognitive reserve in non-e4 carriers. Future studies should explore other potential factors of resiliency (e.g., diet, exercise) and examine the association between genetic risk and social support on neural markers (e.g., cortical thinning, hippocampal atrophy).

Agronomic performance and yield stability of extra-early maturing maize hybrids in multiple environments in the Sahel

Frequent occurrence of drought, heat, low soil fertility and Striga infestation are the main stress factors reducing maize yield in the Sahel. Adoption of stable multiple stress tolerant maize cultivars in the region is crucial for achieving food security. However, selection of a stable high yielding cultivar is complicated by genotype × environment interaction (GEI) due to differential responses to growing conditions. Eleven extra-early maturing multiple-stress tolerant maize hybrids and two checks arranged in a randomized complete block design was evaluated across nine locations for two years in Mali and Niger. The objectives of this study were to identify (i) stable and high-yielding maize hybrids, and (ii) suitable test locations for selecting promising extra-early maize hybrids. GGE biplot was used for graphical analysis. Significant genotype, location and GEI effects were detected for grain yield and number of ears per plant. EEWQH-13 produced the highest grain yield (3860 kg ha−1) while EEYQH-1 had the poorest yield (2663 kg ha−1) with trial mean of 3395 kg ha−1 for all hybrids. GGE biplot explained 69.6 % of the total variation in grain yield among the hybrids. The polygon view identified EEWQH-13 as the best hybrid across six of the nine test locations. EEPVAH-58 was identified as the most stable high yielding hybrid across the nine test locations followed by EEWQH-16 and EEWQH-13. The nine locations were clustered under two mega-environments (ME1, ME2). Among the nine test locations, Tara and Aderaoua clustered in ME1 were the most suitable ones for selecting promising extra-early maize hybrids for wider adaptation. The three hybrids, EEPVAH-58, EEWQH-16, and EEWQH-13, identified in this study could be recommended for on-farm evaluation to confirm the consistency of their yield performance for possible release and commercialization in Mali and Niger.

Peripheral and Placental Prevalence of Sulfadoxine-Pyrimethamine Resistance Markers in Plasmodium falciparum among Pregnant Women in Southern Province, Rwanda.

Intermittent preventive therapy during pregnancy (IPTp) with sulfadoxine-pyrimethamine (SP) is recommended in areas of moderate to high malaria transmission intensity. As a result of the increasing prevalence of SP resistance markers, IPTp-SP was withdrawn from Rwanda in 2008. Nonetheless, more recent findings suggest that SP may improve birthweight even in the face of parasite resistance, through alternative mechanisms that are independent of antimalarial effects. The prevalence of single nucleotide polymorphisms in Plasmodium falciparum dihydropteroate synthase (pfdhps) and dihydrofolate reductase (pfdhfr) genes associated with SP resistance among 148 pregnant women from 2016 to 2018 within Rwanda's Southern Province (Huye and Kamonyi districts) was measured using a ligase detection reaction-fluorescent microsphere assay. The frequency of pfdhps K540E, A581G, and the quintuple (pfdhfr N51I + C59R + S108N/pfdhps A437G + K540E) and sextuple (pfdhfr N51I + C59R + S108N/pfdhps A437G + K540E + A581G) mutant genotypes was 90%, 38%, 75%, and 28%, respectively. No significant genotype difference was seen between the two districts, which are approximately 50 km apart. Observed agreements for matched peripheral to placental blood were reported and found to be 207 of 208 (99%) for pfdhfr and 239 of 260 (92%) for pfdhps. The peripheral blood sample did not miss any pfdhfr drug-resistant mutants or pfdhps except at the S436 loci. At this level of the sextuple mutant, the antimalarial efficacy of SP for preventing low birthweight is reduced, although overall SP still exerts a nonmalarial benefit during pregnancy. This study further reveals the need to intensify preventive measures to sustain malaria control in Rwanda to keep the overall incidence of malaria during pregnancy low.

Root Distribution, Agronomic Performance, and Phosphorus Utilization in Wheat as Mediated by Phosphorus Placement under Rainfed Coastal Saline Conditions

Rainfall variations between seasons could affect phosphorus translocation from rainfed saline soil to wheat plants. Whether deep-banded P application increases wheat yield compared to traditional P placement under rainfed coastal saline conditions remains a question. This study investigated the impact of season, P placement, and genotype on root distribution, agronomic performance, and P utilization in wheat grown under rainfed coastal saline conditions. Four wheat genotypes (two tall genotypes (Alice and Shavano) and two dwarf genotypes (AK58 and LX99)) were grown in a saline field with five P placement treatments (Top-dressed High P input (TopHP), Deep-banded High P input (DeepHP), Top-dressed Reduced P input (TopRP), Deep-banded Reduced P input (DeepRP), and no P supply (No P)) for two consecutive seasons. Root length density (RLD), agronomic traits, nutrient concentrations in grain and straw, and P utilization efficiency were determined. Statistical analysis was employed to compare the P utilization across treatments. TopHP increased RLD at a 0–20 cm depth, while deep-banded P increased RLD at a 20–40 cm depth. The wet season (2021–2022) resulted in higher grain yields, more fertile spikelets, and fewer non-fertile spikelets in all four genotypes than the dry season (2020–2021). The highest 1000-kernel weights occurred in DeepHP or TopHP. Deep-banded P outperformed top-dressed P placement in terms of P utilization efficiency for LX99, Shavano, and AK58 (not Alice) in both seasons. Nutrient concentrations/accumulations showed inconsistent patterns due to significant genotype × P placement interactions. PCA analysis revealed that first two PCs accounted for 56.19% and 60.13% of the variance in the 2020–2021 and 2021–2022 seasons, respectively. The first component (PC1) represented root spatial distribution and straw weight, while the second component (PC2) represented 1000-kernel weight, grain number per head, and grain yield. Altered P utilization efficiency mediated by P placement was associated with changes in wheat root distribution, agronomic traits, and nutrient concentrations in straw and grain. The increased wheat yield in the wet season (2021–2022) was attributed to higher rainfall.

A Multi-Model Based Stability Analysis Employing Multi-Environmental Trials (METs) Data for Discerning Heat Tolerance in Chickpea (Cicer arietinum L.) Landraces.

Identifying a congenially targeted production environment and understanding the effects of genotype by environmental interactions on the adaption of chickpea genotypes is essential for achieving an optimal yield stability. Different models like additive main effect and multiplicative interactions (AMMI 1, AMM2), weighted average absolute scores of BLUPs (WAASB), and genotype plus genotype-environment (GGE) interactions were used to understand their suitability in the precise estimation of variance and their interaction. Our experiment used genotypes that represent the West Asia-North Africa (WANA) region. This trial involved two different sowing dates, two distinct seasons, and three different locations, resulting in a total of 12 environments. Genotype IG 5871(G1) showed a lower heat susceptibility index (HSI) across environments under study. The first four interactions principal component axis (IPCA) explain 93.2% of variations with significant genotype-environment interactions. Considering the AMMI stability value (ASV), the genotypes IG5862(G7), IG5861(G6), ILC239(G40), IG6002(G26), and ILC1932(G39), showing ASV scores of 1.66, 1.80, 2.20, 2.60, and 2.84, respectively, were ranked as the most stable and are comparable to the weighted average absolute scores of BLUPs (WAASB) ranking of genotypes. The which-won-where pattern of genotype plus genotype-environment (GGE) interactions suggested that the target environment consists of one mega environment. IG5866(G10), IG5865(G9), IG5884(G14), and IG5862(G7) displayed higher stability, as they were nearer to the origin. The genotypes that exhibited a superior performance in the tested environments can serve as ideal parental lines for heat-stress tolerance breeding programs. The weighted average absolute scores of BLUPs (WAASB) serve as an ideal tool to discern the variations and identify the stable genotype among all methods.

Yield and Mineral Composition among Mungbean [Vigna radiata (L.) R. Wilczek] Genotypes Grown in Different Agroecologies in East Africa

Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] also referred to as green gram is a key crop especially in the marginal areas of East Africa. It is rich in micronutrients and protein and thus can help ameliorate malnutrition if incorporated into diets. This study was conducted to evaluate the performance of 26 fixed elite mungbean breeding genotypes for yield and micronutrient composition across different locations in East Africa (Uganda, Kenya, and Tanzania). The genotypes displayed significant variability for nutritional, phenology, and yield-related traits across test environments. Significant genotype effects were observed for most of the traits except for average yield per plant and dry matter content ( P < 0.05). Random effect of environment was significant for all traits, and significant GXE was observed for all traits except for dry matter and iron content ( P < 0.05). Moderate to high broad-sense heritability (H2) was found among traits except for dry matter content which was low (H2 = 10.4%). There was a significant and positive correlation between Fe and Zn (r = 0.58), and Fe and Ca (r = 0.46), indicating the potential to enhance these traits simultaneously through breeding and/or selection. However, the correlation between yield and nutrients (iron, zinc, and calcium) was negative. Environments KAT_SR_2019, KYM_LR_2020, and KYM_LR_2020 were found to be discriminating (informative) and representative of grain yield, calcium, and zinc content, respectively. Genotypes AVMU 1679, AVMU 1685, and AVMU1686 combined both stability and high micronutrient content, while the high yielding and stable genotypes were AVMU 1689, AVMU 1681, and AVMU 16102. The identified genotypes need to be assessed for farmer preference in on-farm trials before they can be recommended for release as new varieties. Additionally, these genotypes will be useful in future breeding efforts as donors aimed at developing nutrient-dense and high yielding mungbean varieties.

Understanding the combining ability of nutritional, agronomic and industrial traits in soybean F2 progenies

Obtaining soybean genotypes that combine better nutrient uptake, higher oil and protein levels in the grains, and high grain yield is one of the major challenges for current breeding programs. To avoid the development of unpromising populations, selecting parents for crossbreeding is a crucial step in the breeding pipeline. Therefore, our objective was to estimate the combining ability of soybean cultivars based on the F2 generation, aiming to identify superior segregating parents and populations for agronomic, nutritional and industrial traits. Field experiments were carried out in two locations in the 2020/2021 crop season. Leaf contents of the following nutrients were evaluated: phosphorus, potassium, calcium, magnesium, sulfur, copper, iron, manganese, and zinc. Agronomic traits assessed were days to maturity (DM) and grain yield (GY), while the industrial traits protein, oil, fiber and ash contents were also measured in the populations studied. There was a significant genotype × environment (G × A) interaction for all nutritional traits, except for P content, DM and all industrial traits. The parent G3 and the segregating populations P20 and P27 can be used aiming to obtain higher nutritional efficiency in new soybean cultivars. The segregating populations P11 and P26 show higher potential for selecting soybean genotypes that combine earliness and higher grain yield. The parent G5 and segregant population P6 are promising for selection seeking improvement of industrial traits in soybean.

Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats.

Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. The work aimed to search for candidate genes related to body measurements and body weight of Karachai goats and develop an experimental PCR-RV test system for genotyping significant SNPs. Comparison of GWAS results for ages 4 and 8 months revealed 58 common SNPs for significant genotypes. 11 common SNPs were identified for body weight, 4 SNPs-for group of traits withers height, rump height, body length, 2 SNPs-for withers height and rump height, 1 SNP-for body length and chest depth. Structural annotation of genomic regions covering a window of ±0.20 Mb showed the presence of 288 genes; 52 of them had the described functions in accordance with gene ontology. The main molecular functions of proteins encoded by these genes are the regulation of transcription, cell proliferation, angiogenesis, body growth, fatty acid and lipid metabolism, nervous system development, and spermatogenesis. SNPs common to body weight and localized within a window of ±200 kb from the structural genes CRADD, HMGA2, MSRB3, FUT8, MAX, and RAB15 were selected to create a test system. The study of meat productivity after slaughter and chemical analysis of muscle tissue in Karachai goats at the age of 8 months of different genotypes according to the identified SNPs revealed that rs268269710 is the most promising for further research and use in breeding. The GG genotype is associated with a larger live weight of animals, a larger carcass yield, the content of the boneless part in it, and the ratio of protein and adipose tissue in meat preferred for dietary nutrition. These results will contribute to the genetic improvement of Karachai goats.

ПОРОДНІ ОСОБЛИВОСТІ АЛЕЛЬНОГО ПРОФІЛЮ ГЕНІВ PIT1 ТА GH УКРАЇНСЬКОЇ АБОРИГЕННОЇ ЛЕБЕДИНСЬКОЇ ПОРОДИ КОРІВ

The preservation of genetic diversity is a paramount concern in addressing global challenges today. The foundation of biological diversity hinges on its genetic components, and the loss of species and genetic variability poses a genuine threat to the biosphere. This is because the sustainability of natural ecosystems and agroecosystems depends directly on their genetic adaptability to changing environmental conditions.
 In cattle, genes associated with milk yield play a crucial role, including genes related to milk proteins and hormones. Among these, the pituitary-specific transcription factor (PIT1) and growth hormone (GH) genes are of particular significance. In this study, we investigated the polymorphism of these genes in the Lebedyn breed of cattle.
 A total of 2 gene polymorphisms, PIT1 and GH, were examined through molecular and genetic research conducted at the genetics laboratory of the Institute of Animal Breeding and Genetics named after M. V. Zubets, part of the National Academy of Agrarian Science of Ukraine. The study utilized 32 DNA samples extracted from the venous blood of Lebedyn breed cows using the 'DNA Sorb-B' kit from AmpliSens. Genotyping was carried out through polymerase chain reaction (PCR-RFLP) analysis of restriction fragment length polymorphism, employing the “Tertsyk” amplifier for PCR. The resulting DNA restriction analysis products were assessed via electrophoresis in a 2–3% agarose gel containing ethidium bromide, with DNA fragment lengths determined using the GeneRuler TM 50 bp DNA Ladder and Thermo Scientific™ GeneRuler 1 kb Plus DNA Ladder markers.
 For the PIT1 gene analysis, a 451 bp amplified fragment was treated with the enzyme HinfI, yielding the following allele frequencies: A (0.38) and B (0.62). The heterozygous AB genotype was the most prevalent (0.45), while homozygotes for the A allele constituted 0.15 of the population. In the case of the GH gene fragment (223 bp), hydrolysis was performed using the restriction enzyme AluI. Analysis of allele frequency distribution indicated a high frequency of the L allele (0.85), with no animals exhibiting the homozygous GHVV genotype, and the GHLL genotype was present in 0.7 of the population.
 These findings reveal unique features of the allelic spectrum of the PIT1 (V-0.62) and GH (L-0.85) genes specific to the Ukrainian indigenous Lebedyn breed of cows. Selectionally significant genotypes include PIT1AA (15%) and GHLL (70%), while heterozygote carriers, which contribute to genetic diversity within the population, account for 45% and 30%, respectively.
 This study’s results hold particular value due to the alarming decline in the population of local indigenous breeds and the imminent threat to the preservation of agricultural genetic resources.

Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet

Pearl millet (Pennisetum glaucum [L.] R. Br.) is a nutrient-dense, relatively drought-tolerant cereal crop cultivated in dry regions worldwide. The crop is under-researched, and its grain yield is low (< 0.8 tons ha−1) and stagnant in the major production regions, including Burkina Faso. The low productivity of pearl millet is mainly attributable to a lack of improved varieties, Striga hermonthica [Sh] infestation, downy mildew infection, and recurrent heat and drought stress. Developing high-yielding and Striga-resistant pearl millet varieties that satisfy the farmers’ and market needs requires the identification of yield-promoting genes linked to economic traits to facilitate marker-assisted selection and gene pyramiding. The objective of this study was to undertake genome-wide association analyses of agronomic traits and Sh resistance among 150 pearl millet genotypes to identify genetic markers for marker-assisted breeding and trait introgression. The pearl millet genotypes were phenotyped in Sh hotspot fields and screen house conditions. Twenty-nine million single nucleotide polymorphisms (SNPs) initially generated from 345 pearl millet genotypes were filtered, and 256 K SNPs were selected and used in the present study. Phenotypic data were collected on days to flowering, plant height, number of tillers, panicle length, panicle weight, thousand-grain weight, grain weight, number of emerged Striga and area under the Striga number progress curve (ASNPC). Agronomic and Sh parameters were subjected to combined analysis of variance, while genome-wide association analysis was performed on phenotypic and SNPs data. Significant differences (P < 0.001) were detected among the assessed pearl millet genotypes for Sh parameters and agronomic traits. Further, there were significant genotype by Sh interaction for the number of Sh and ASNPC. Twenty-eight SNPs were significantly associated with a low number of emerged Sh located on chromosomes 1, 2, 3, 4, 6, and 7. Four SNPs were associated with days-to-50%-flowering on chromosomes 3, 5, 6, and 7, while five were associated with panicle length on chromosomes 2, 3, and 4. Seven SNPs were linked to thousand-grain weight on chromosomes 2, 3, and 6. The putative SNP markers associated with a low number of emerged Sh and agronomic traits in the assessed genotypes are valuable genomic resources for accelerated breeding and variety deployment of pearl millet with Sh resistance and farmer- and market-preferred agronomic traits.

Resiliency of fast-growing and slow-growing genotypes of broiler chickens submitted to different environmental temperatures: growth performance and meat quality

Growth performance and meat quality were assessed in 238 chicks of both sexes belonging to a commercial crossbreed (Ross 308), and 2 Italian local breeds (Bionda Piemontese-BP and Robusta Maculata-RM). The chickens were kept in 2 rooms at standard environmental conditions or under heat stress (+4.7°C on average) until slaughtering (42 d of age for Ross 308 and 99 d for RM and BP chickens). The Ross chickens showed the highest final live weight, feed intake, and daily weight gain, and the best feed conversion ratio compared to the local breeds (P < 0.001), with RM performing better than BP chickens. Thus, Ross chickens had the heaviest carcasses, the highest slaughter, and breast yields followed by RM and BP chickens (P < 0.001). At the pectoralis major (p. major) muscle, Ross chickens showed the highest pH, lightness, and yellowness, besides the highest cooking losses, whereas BP showed the highest redness (P < 0.001). Ross meat had higher water and ether extract contents, and lower crude protein content compared to BP and RM (P < 0.001), whereas no differences among genotypes were measured for the fatty acid profile. At the sensory analysis, Ross breasts had a higher juiciness compared to BP ones, besides a lower score for "brothy and chickeny/meaty" and a higher one for "wet feathers" compared to local breeds (0.05 < P < 0.001). The increase of the room temperature decreased growth performance and cold carcass weight (P < 0.001) compared to standard conditions, whereas the rate of α-linolenic acid in the meat increased (P < 0.01). The effect of a high environmental temperature on growth performance and slaughter and meat quality traits was more pronounced in Ross compared to BP and RM chickens (0.05 < P <0.001; significant interaction genotype×temperature). In conclusions, local chicken breeds showed lower performance and slaughter yield compared to the commercial genotype, but more favorable meat quality traits and higher resilience to the environmental heat-stress.

Геногеография фармакогенетически значимых ДНК-маркеров CYP2C19 суперсемейства цитохромов в народонаселении России и сопредельных стран

Genetic testing of each patient aimed at detecting the pharmacogenetic marker carrier state is challenging for healthcare system. However, knowledge about the frequencies of pharmacogenetically important genes enables making decisions about treatment based on the patient’s ethnicity. The CYP2C19 cytochrome gene involved in biotransformation of a broad spectrum of drugs is one of the most important. The study was aimed to determine the frequencies of major CYP2C19 variants and the patterns of their spatial variability in the population of Russia. The database Pharmacogenetics of the Population of Russia and Neighboring Countries created by the research team was used to determine frequencies of the CYP2C19 *1, *2, *3, *17 variants and their genotypes: *1 – 53 populations, n = 2261 samples; *2 — 79 populations, n = 6346; *3 — 92 populations, n = 7517; *17 — 35 populations, n = 3313. We have created a cartographic atlas that includes the *1, *2, *3, *17 frequency maps, correlation maps, and genotype frequency maps. Specific data on the frequencies of CYP2C19 variants and their pharmacogenetically significant genotypes in the major ethnic groups of Russia are provided. The cartographic atlas enables prediction of frequencies of significant CYP2C19 variants and their genotypes in the peoples, information about which is currently missing. The *1 and *2 variants gene geography is characterized by similar pattern: the combination of longitudinal trend of frequency increase from west to southeast and latitudinal variability of frequency increase from north to south in the Asian part of the region. Variant *3 is characterized by the clear longitudinal vector of frequency increase from 0 in the west to the world’s maximum in the Amur region. Variant *17 shows a pronounced longitudinal trend with the oppositely directed vector of frequency decrease from west to southeast. The correlation maps indicate regions, where the similarity between core patterns is disrupted.

A multifaceted interplay between virulence, drug resistance, and the phylogeographic landscape of Mycobacterium tuberculosis.

Latin-American Mediterranean (LAM) family is one of the most significant and global genotypes of Mycobacterium tuberculosis. Here, we used the murine model to study the virulence and lethality of the genetically and epidemiologically distinct LAM strains. The pathobiological characteristics of the four LAM strains (three drug resistant and one drug susceptible) and the susceptible reference strain H37Rv were studied in the C57BL/6 mouse model. The whole-genome sequencing was performed using the HiSeq Illumina platform, followed by bioinformatics and phylogenetic analysis. The susceptible strain H37Rv showed the highest virulence. Drug-susceptible LAM strain (spoligotype SIT264) was more virulent than three multidrug-resistant (MDR) strains (SIT252, SIT254, and SIT266). All three MDR isolates were low lethal, while the susceptible isolate and H37Rv were moderately/highly lethal. Putting the genomic, phenotypic, and virulence features of the LAM strains/spoligotypes in the context of their dynamic phylogeography over 20 years reveals three types of relationships between virulence, resistance, and transmission. First, the most virulent and more lethal drug-susceptible SIT264 increased its circulation in parts of Russia. Second, moderately virulent and pre-XDR SIT266 was prevalent in Belarus and continues to be visible in North-West Russia. Third, the low virulent and MDR strain SIT252 previously considered as emerging has disappeared from the population. These findings suggest that strain virulence impacts the transmission, irrespective of drug resistance properties. The increasing circulation of susceptible but more virulent and lethal strains implies that personalized TB treatment should consider not only resistance but also the virulence of the infecting M. tuberculosis strains. IMPORTANCE The study is multidisciplinary and investigates the epidemically/clinically important and global lineage of Mycobacterium tuberculosis, named Latin-American-Mediterranean (LAM), yet insufficiently studied with regard to its pathobiology. We studied different LAM strains (epidemic vs endemic and resistant vs susceptible) in the murine model and using whole-genome analysis. We also collected long-term, 20-year data on their prevalence in Eurasia. The findings are both expected and unexpected. (i) We observe that a drug-susceptible but highly virulent strain increased its prevalence. (ii) By contrast, the multidrug-resistant (MDR) but low-virulent, low-lethal strain (that we considered as emerging 15 years ago) has almost disappeared. (iii) Finally, an intermediate case is the MDR strain with moderate virulence that continues to circulate. We conclude that (i) the former and latter strains are the most hazardous and require close epidemiological monitoring, and (ii) personalized TB treatment should consider not only drug resistance but also the virulence of the infecting strains and development of anti-virulence drugs is warranted.

Sulla (Hedysarum coronarium L.) Response to Drought Stress during Early Vegetative Stage.

Sulla (Hedysarum coronarium L.) is a Mediterranean biannual anthelmintic forage. Due to its high productivity, nutraceutical value, and suitability for harsh environments, interest in this crop is growing. Under the current scenario of climate change and water scarcity, it is important to evaluate crop drought tolerance, especially for newly bred materials. Drought stress and well-watered conditions (50 vs. 80% of the field capacity) were applied in a pot experiment to compare responses of the widespread commercial variety Bellante with those of a recently released variety named 'Centauro', currently registered in the Italian national register of plant varieties but not yet available on the market. Compared to the well-watered treatment, drought-stressed plants showed lower values of fresh biomass (-69%), number of leaves (-68%), and root length (-49%). The Centauro cv. showed a different architecture to Bellante with more shoots (+43% P < 0.05) and a trend for more leaves (+25% P = 0.08). These traits are possibly related to its superior palatability. Centauro also developed a higher root length (+70%, P < 0.05) across irrigation levels. Drought stress affected condensed tannin (CT) content. A significant genotype × environment interaction was found with Centauro displaying more (+50%) and less (-35%) CT than Bellante under drought stress and well-watered conditions, respectively. The higher constitutive root length density of Centauro may be exploited in breeding programs aimed at improving the root sink, given the role of this trait in resource acquisition capacity and root-derived ecosystem services.

Genotypic variability and genetic parameters for root yield, dry matter and related traits of cassava in the Guinea Savannah ecological zone of Ghana

The aim of this study was to assess the agronomic performance and genetic parameters governing storage root yield and related traits in cassava genotypes in order to identify superior genotypes. The study involved 18 elite cassava genotypes which were arranged in a randomized complete block design with three replications and assessed for storage root yield and yield components (12 months after planting) in the Guinea savannah ecology of Ghana for three seasons. Analysis of variance indicated significant (p &lt; 0.05) genotype and year main effects for fresh and dry root yields, dry matter content, starch yield and harvest index. Genotype × year effect was significant (p &lt; 0.05) for fresh root yield, dry root yield and starch yield. Estimates of the variance components revealed greater genotypic influence for starch yield, fresh and dry root yields implying the potential for genetic gain with selection for these traits among the genotypes. Relatively high (69 %) broad sense heritability estimate was observed for dry storage root yield indicating the depth of genetic influence. Path coefficient analysis revealed a direct positive effect of dry matter content on dry storage root yield whilst dry storage root yield had direct positive effect on starch yield suggesting the possibility of indirect selection for starch yield through dry storage root yield. The study revealed ample genotypic variability among the cassava genotypes to warrant selection. Four genotypes, IBA 070134, IBA 419, IBA 950289 and IBA 980581 were identified for high and stable fresh and dry root yields for multilocational testing.

Identification of single nucleotide polymorphisms (SNPs) associated with chronic graft-versus-host disease in patients undergoing allogeneic hematopoietic cell transplantation

IntroductionChronic graft-versus-host disease (cGVHD) is a debilitating side effect of allogeneic hematopoietic cell transplantation (HCT), affecting the quality of life of patients. We used whole exome sequencing to identify candidate SNPs and complete a multi-marker gene-level analysis using a cohort of cGVHD( +) (N = 16) and cGVHD( −) (N = 66) HCT patients.MethodsSaliva samples were collected from HCT patients (N = 82) pre-conditioning in a multi-center study from March 2011 to May 2018. Exome sequencing was performed and FASTQ files were processed for sequence alignments. Significant SNPs were identified by logistic regression using PLINK2v3.7 and Fisher’s exact test. One cGVHD( −) patient sample was excluded from further analysis since no SNP was present in at least 10% of the sample population. The FUMA platform’s SNP2GENE was utilized to annotate SNPs and generate a MAGMA output. Chromatin state visualization of lead SNPs was completed using Epilogos tool. FUMA’s GENE2FUNC was used to obtain gene function and tissue expression from lead genomic loci.ResultsLogistic regression classified 986 SNPs associated with cGVHD( +). SNP2GENE returned three genomic risk loci, four lead SNPs, 48 candidate SNPs, seven candidate GWAS tagged SNPs, and four mapped genes. Fisher’s exact test identified significant homozygous genotypes of four lead SNPs (p < 0.05). GENE2FUNC analysis of multi-marker SNP sets identified one positional gene set including lead SNPs for KANK1 and KDM4C and two curated gene sets including lead SNPs for PTPRD, KDM4C, and/or KANK1.ConclusionsOur data suggest that SNPs in three genes located on chromosome 9 confer genetic susceptibility to cGVHD in HCT patients. These genes modulate STAT3 expression and phosphorylation in cancer pathogenesis. The findings may have implications in the modulation of pathways currently targeted by JAK inhibitors in cGVHD clinical trials.

Effects of Plant Growth Promoting Rhizospheric Bacteria (PGPR) on Survival, Growth and Rooting Architecture of Eucalyptus Hybrid Clones

Clonal plantation involves the rooting of cuttings from superior genotypes selected for their hybrid vigor and desired qualities. However, the cuttings of some Eucalyptus species and their hybrid genotypes present difficulties in their rooting capacity. Applying PGPR to cutting growth medium as a root stimulating agent has not been extensively studied for Eucalyptus tree species. We aimed to assess the rooting capacity of cuttings taken from two poor-rooting Eucalyptus hybrid clones of E. grandis × E. nitens through the application of PGPR in nursery trials. Seven rhizospheric bacterial species that demonstrated the ability to produce indole-3-acetic acid and to solubilise phosphate were used to prepare two rhizospheric consortium inoculums in which Pseudomonas-Bacillus strains and non-Pseudomonas-Bacillus were grouped. Inoculums were tested for their rooting stimulating capacity on cuttings of the hybrids GN 018B and GN 010 and compared to the nursery standard indole-3-butyric acid. A total of 320 cuttings were treated. Both hybrid clones demonstrated significant (p &lt; 0.0001) genotype differences for all three growth responses, i.e., total, root, and shoot length. Cuttings of both hybrids demonstrated high survival rates and rooting percentage. Although several rooting architectural configurations were prevalent, the Pseudomonas-Bacillus consortium promoted adventitious root development and fibrosity in GN 018B hybrids.