Estimation of Gene Action for Seed Yield and Component Traits using Generation Mean Analysis in Pigeonpea [Cajanus cajan (L.) Millspaugh]

Background: For improvement of quantitative traits the information on nature of gene action is an important asset for plant breeders. However, the information on gene action for yield and its attributes is scanty in pigeonpea crop. Methods: The present experiment was carried out during kharif 2018-2020 at GBPUAT, Pantnagar, Uttarakhand. The experimental material consisted of six generations of three crosses viz., PADT-16 × PUSA 992, PADT-16 × UPAS 120 and PADT-16 × PAU 881. The observations were recorded on nine morphological characters. The gene action was estimated by three parameters model of Jinks and Jones if scaling tests were non significant and six parameters model of Hayman if scaling tests were significant. Result: For majority of traits in all three crosses, epistatic gene action was present as scaling tests were found to be significant. However, for traits number of primary branches, number of secondary branches and number of seeds per pod in cross PADT-16 × UPAS 120 a simple additive/dominance model was found to be adequate. In general, magnitude of dominance was found to be higher as compared to corresponding additive gene action. The high magnitude of dominance indicated that heterosis breeding is rewarding in these characters.

Estimation of Gene Action and Interaction for Some Quantitative Characters in Rice (Oryza sativa L.) by Generation Mean Analysis

The present investigation was conducted to understand the genetic action for controlling the inheritance of some quantitative characters. The experimental materials consisted of three rice varieties, i.e., Mahsuri, Bhutmuri, IR36 and F1, F2, and F3 populations of Mahsuri×Bhutmuri (Cross I) and IR36×Bhutmuri (Cross II). To conduct the generation mean analysis, the parents and their F1, F2, and F3 populations were evaluated during June to October month of Kharif 2016 and Kharif 2017. Generation mean analysis was done for eighteen quantitative characters following the five parameter model. The Analysis of Variance revealed significant differences among the five generations for all the characters studied. The results of the scaling tests and joint scaling test revealed that the Simple additive-dominance model was inadequate for days to 50% flowering, days to maturity, number of panicles plant-1, number of primary branches panicle-1, number of secondary branches panicle-1 in Cross I, while it was for plant height, number of tillers plant-1, number of panicles plant-1, number of grains panicle-1, number of filled grains panicle–1 and fertility % in Cross II. Hence, the present studies have revealed that epistasis as a basic mechanism that cannot be ignored. Thus, formulating breeding policies on only main gene effects i.e. additive and dominance could be misleading.

Asymmetry drives the cumulative impacts of multiple stressors on freshwater ecosystems under a warming climate

Climate warming is an important stressor in freshwater ecosystems, yet its interactive effects with other environmental changes are poorly understood. We address this challenge by testing the ability of three contrasting null models to predict the joint impacts of warming and a second stressor using a new database of 296 experimental combinations. Despite concerns that stressors will interact to cause synergisms, we found that net impacts were best explained by the effect of the worst stressor (the dominance null model). When this stressor’s impact was at least 50% greater than that of the second, the dominance model was most accurate in 62% of responses. Prediction accuracy depended on the identity of the stressors and declined at higher levels of biological organisation. Together these findings suggest we can often effectively forecast impacts of multiple stressors by focusing on the degree of asymmetry that exists among their independent impacts.

Effect of NPC1L1 and HMGCR Genetic Variants With Premature Triple-Vessel Coronary Disease

Background: Both Niemann-Pick C1-like 1 (NPC1L1) and 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) play a key role on dyslipidaemia. We aim to evaluate whether NPC1L1 and HMGCR genetic variants are associated with susceptibility of premature triple-vessel disease (PTVD).Methods: Four single-nucleotide polymorphisms (SNPs) (rs11763759, rs4720470, rs2072183, and rs2073547) of NPC1L1; and three SNPs (rs12916, rs2303151, and rs4629571) of HMGCR were genotyped in 872 PTVD patients (males ≤ 50 years old and females ≤ 60 years old), and 401 healthy controls.Results: After adjusting for age and sex, rs12916 of HMGCR was associated with the risk of PTVD in dominance model [odds ratio (OR) = 1.68, 95% confidence intervals (CI): 1.29–2.18, P < 0.001], recessive model (OR = 1.43, 95% CI: 1.08–1.90, P = 0.013) and codominant model (OR = 1.38, 95% CI: 1.17–1.63, P < 0.001); meanwhile, rs4720470 of NPC1L1 was related to increased risk of PTVD in recessive model (OR = 1.74, 95% CI: 1.14–2.74, P = 0.013). Patients who carried both variant rs4720470 and rs12916 also had the risk of PTVD (P < 0.001); however, there were no correlation between these SNPs and the SNYTAX score (all P > 0.05).Conclusions: This is the first report that rs4720470 is a novel polymorphism of the NPC1L1 gene associated with PTVD, and rs12916 of HMGCR gene appears to be a strong genetic marker of PTVD. Our study may improve the early warning, therapeutic strategies and drug development of PTVD.

The Influence of ICAM1 3 ′ UTR Gene Polymorphism on the Occurrence and Metastasis of Primary Liver Cancer

Objective. In this study, we explored the influence of single nucleotide polymorphism (SNP) in the noncoding region of intercellular adhesion molecule 1 (ICAM1) gene on the occurrence and metastasis of primary hepatocellular carcinoma (PHC). Methods. Sanger sequencing was used to analyze the genotypes of rs3093032, rs923366, and rs281437 locus in the 3 ′ untranslated region (UTR) of the ICAM1 gene. The level of plasma ICAM1 was analyzed by enzyme-linked immunosorbent assay (ELISA). Results. After adjusting for risk factors such as BMI, smoking, drinking, family history of tumors, and hepatitis B virus test results, the CT genotype at rs3093032 of the ICAM1 gene ( OR = 0.19 , 95% CI: 0.08-0.44, P < 0.01 ), dominance model ( OR = 0.23 , 95% CI: 0.11-0.48, P < 0.01 ), and T allele ( OR = 0.27 , 95% CI: 0.14-0.53, P < 0.01 ) were related to the reduced risk of PHC susceptibility. rs923366 locus CT genotype ( OR = 0.63 , 95% CI: 0.44-0.90, P = 0.01 ), TT genotype ( OR = 0.23 , 95% CI: 0.10-0.53, P < 0.01 ), dominant model ( OR = 0.55 , 95% CI: 0.39-0.77, P < 0.01 ), recessive model ( OR = 0.28 , 95% CI: 0.12-0.62, P < 0.01 ), and T allele ( OR = 0.55 , 95% CI: 0.42-0.73, P < 0.01 ) were related to a reduction in the risk of PHC susceptibility. rs281437 locus CT genotype ( OR = 2.08 , 95% CI: 1.40-3.09, P < 0.01 ), TT genotype ( OR = 5.20 , 95% CI: 2.22-12.17, P < 0.01 ), dominant model ( OR = 2.45 , 95% CI: 1.69-3.54, P < 0.01 ), recessive model ( OR = 4.32 , 95% CI: 1.86-10.06, P < 0.01 ), and T allele ( OR = 2.46 , 95% CI: 1.79-3.38, P < 0.01 ) were significantly related to the increased risk of PHC susceptibility. SNPs at rs3093032, rs923366, and rs281437 of the ICAM1 gene were significantly correlated with TNM stage and tumor metastasis of PHC patients ( P < 0.05 ). Conclusion. SNPs at rs3093032, rs923366, and rs281437 in the 3 ′ UTR region of the ICAM1 gene are related to the occurrence and metastasis of PHC.

The impact of linkage disequilibrium and epistasis in the studies of inheritance based on Hayman’s diallel and generation mean analysis

This simulation-based study assessed the impact of linkage disequilibrium (LD) and epistasis on Hayman’s diallel and generation mean analysis, assuming hundreds of genes, variable degree of dominance, and seven types of digenic epistasis. The diallel parents were 15 doubled-haploid lines from a high LD population. The generation mean analysis was based on seven generations, assuming association. Under low LD and no epistasis, the diallel analysis provided confident results about the inheritance of the quantitative trait and high correlation between number of recessive genes and Wr + Vr, but biased estimates of the dominance components and genetic parameters. The additional consequences of high LD under no epistasis were rejection of the additive-dominance model assuming high heritability and lower correlation. Assuming 100% of epistatic genes, for four epistasis types there was evidence of inadequacy of the additive-dominance model. Assuming 30% of epistatic genes, there was a tendency for accepting the additive-dominance model for low heritability traits and for rejecting for high heritability traits. Linkage and epistasis affects the estimates of the genetic components of the generation means. Even assuming 100% of interacting genes, for most epistasis types there was no statistical evidence of epistasis. Assuming positive partial dominance, the signs of the epistatic components do not allow discriminate complementary, recessive, dominant and recessive, duplicate genes with cumulative effects, and non-epistatic genic interaction. Negative epistatic components evidence dominant epistasis. When the additive x additive and dominance x dominance components are positive and the additive x dominance component is negative, there is duplicate epistasis.

Polymorphisms of Fatty Acid Elongase 2 Gene Afftects Risk of Pulmonary Tuberculosis in China Han Population

Background: As an infectious disease closely related to Mycobacterium tuberculosis, autoimmunity, inflammation, environment and heredity, the relationship between the single nucleotide polymorphism of elongase 2 gene and the susceptibility to tuberculosis is still unknown. Methods: Between January 2016 and November 2018, a hospital-based case-control study was conducted. This epidemiological survey was conducted in both hospitals every three months. rs3798719, rs1570069, and rs2236212 in ELOVL2 gene were detected by Sanger sequencing. Results: Stratified by gender, the genotypes and allele frequencies of rs3798719, rs1570069 and rs2236212 showed significant differences between the two groups (χ2 = 6.987, P = 0.030), Genetic modeling showed that rs3798719 was statistically different in the overdominance model (χ2 = 4.784, OR = 1.414, 95% CI: 1.036-1.929, P < 0.05). The polymorphism of rs2236212 between male TB patients and healthy controls was statistically different in the dominance model. (χ2 = 4.192, OR = 0.507; 95% CI: 0.262-0.981, P < 0.05). Conclusion: The rs3798719 of ELOVL2 gene may be associated with susceptibility to TB in female population and the rs2236212 of ELOVL2 gene may be associated with TB incidence in male patients.

CYP17A1–ATP2B1 SNPs and Gene–Gene and Gene–Environment Interactions on Essential Hypertension

Background: The association between the CYP17A1 and ATP2B1 SNPs and essential hypertension (referred to as hypertension) is far from being consistent. In addition to the heterogeneity of hypertension resulting in inconsistent results, gene–gene and gene–environment interactions may play a major role in the pathogenesis of hypertension rather than a single gene or environmental factor.Methods: A case–control study consisting of 1,652 individuals (hypertension, 816; control, 836) was conducted in Maonan ethnic minority of China. Genotyping of the four SNPs was performed by the next-generation sequencing technology.Results: The frequencies of minor alleles and genotypes of four SNPs were different between the two groups (p &lt; 0.001). According to genetic dominance model analysis, three (rs1004467, rs11191548, and rs17249754) SNPs and two haplotypes (CYP17A1 rs1004467G-rs11191548C and ATP2B1 rs1401982G-rs17249754A) were negatively correlated, whereas rs1401982 SNP and the other two haplotypes (CYP17A1 rs1004467A-rs11191548T and ATP2B1 rs1401982A-rs17249754G) were positively associated with hypertension risk (p ≤ 0.002 for all). Two best significant two-locus models were screened out by GMDR software involving SNP–environment (rs11191548 and BMI ≥ 24 kg/m2) and haplotype–environment (CYP17A1 rs1004467G-rs11191548C and BMI ≥ 24 kg/m2) interactions (p ≤ 0.01). The subjects carrying some genotypes increased the hypertension risk.Conclusions: Our outcomes implied that the rs1004467, rs11191548, and rs17249754 SNPs and CYP17A1 rs1004467G-rs11191548C and ATP2B1 rs1401982G-rs17249754A haplotypes have protective effects, whereas the rs1401982 SNP and CYP17A1 rs1004467A-rs11191548T and ATP2B1 rs1401982A-rs17249754G haplotypes showed adverse effect on the prevalence of hypertension. Several SNP–environment interactions were also detected.

Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices

Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses were accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).