Quantitative Trait Analysis Research Articles

Genetic Parameters, Correlation and Stability Analysis of Aromatic Rice Landraces of Nepal

Rice is the major food crop directly related to the livelihood of majority of rural people in Nepal. Aromatic rice is one of the fundamental groups that has great significance from the nutritional and market point of view all over the world. The main objective of this study was to emphasize on the determination of major genetic parameters, genotypic and phenotypic correlations, stability analysis for yield and major quantitative traits of aromatic rice landraces. Altogether 30 aromatic rice landraces were considered in this study and that were evaluated in three locations namely Hardinath, Tarahara and Khajura with three replications. Two years of multilocation data on nine morphological traits were collected and evaluated. The genetic parameters like genetic variance, phenotypic variance, genotypic coefficient of variation, phenotypic coefficient of variation, heritability and genetic advance were estimated using the statistical methods. The highest GCV and PCV was exhibited by grain yield (23.67 and 25.7) whereas lowest GCV and PCV was found in panicle length (4.9 and 5.6) respectively. Heritability of various traits was measured from 0.76 to 0.98 where the lowest heritability was observed in panicle length and the highest was observed in both heading and maturity days. The genetic advance as percentage of means value ranging from 8.8 to 45 representing panicle length and grain yield respectively. The genetic correlation of the measured traits showed highly significant positive correlation of heading days with maturity (r=1.0004**) and straw yield (r=0.787**) as well as correlation of maturity days with straw yield (r=0.79**). In case of phenotypic correlation, highly significant positive correlation of heading days with maturity (r=0.99**) and straw yield (r=0.7611**) was obtained however there is negative but significant correlation with tillers per meter square (r=-0.296*), filled grain weight (r=-0.305*), 1000 grain weight (r=0.3115*) and grain yield (r=-0.4*). According to the stability analysis, Gouriya and Karia Kamod (bi=1.1) were found more stable. Based on the value of coefficient of determination (R2), most of accessions; Lalka Basmati, Sugandhit Dha-1, Suhpat, Gouriya, Bayerni Masino, Kalo Nunia, Balamsari Dhan, Tilki, Tulsiful and Sunaulo Sugandha were obtained stable in all the three locations in both years. Based on the Superiority Measure (Pi), Samba Masuli Sub-1 and Sugandhit Dhan-1 showed lower Pi values of 132556.16 to 377994.35 hence identified as most stable varieties. This study identified the genetic parameters that provides the useful information for breeding of rice varieties, correlation among the major traits and stability of some aromatic landraces Gouriya and Karia Kamod obtained in all the environments. Thus, findings of this study are highly helpful for future studies to identify desirable traits and genotypes in the further varietal development works in coming days.

TET2 germline variants promote kidney disease by impairing DNA repair and activating cytosolic nucleotide sensors

Genome-wide association studies (GWAS) have identified over 800 loci associated with kidney function, yet the specific genes, variants, and pathways involved remain elusive. By integrating kidney function GWAS with human kidney expression and methylation quantitative trait analyses, we identified Ten-Eleven Translocation (TET) DNA demethylase 2 (TET2) as a novel kidney disease risk gene. Utilizing single-cell chromatin accessibility and CRISPR-based genome editing, we highlight GWAS variants that influence TET2 expression in kidney proximal tubule cells. Experiments using kidney/tubule-specific Tet2 knockout mice indicated its protective role in cisplatin-induced acute kidney injury, as well as in chronic kidney disease and fibrosis induced by unilateral ureteral obstruction or adenine diet. Single-cell gene profiling of kidneys from Tet2 knockout mice and TET2-knockdown tubule cells revealed the altered expression of DNA damage repair and chromosome segregation genes, notably including INO80, another kidney function GWAS target gene itself. Remarkably, both TET2-null and INO80-null cells exhibited an increased accumulation of micronuclei after injury, leading to the activation of cytosolic nucleotide sensor cGAS-STING. Genetic deletion of cGAS or STING in kidney tubules, or pharmacological inhibition of STING, protected TET2-null mice from disease development. In conclusion, our findings highlight TET2 and INO80 as key genes in the pathogenesis of kidney diseases, indicating the importance of DNA damage repair mechanisms.

Genetic Divergence Analysis for Quantitative Traits in Rice (Oryza sativa L.) Germplasm under Irrigated Conditions

The present study was with the aim of knowing genetic divergence analysis for quantitative traits among the rice genotypes for agronomical and yield traits. The experimental material consists of 36 rice genotypes sown in a Randomized Block Design with three replications and observations recorded on randomly selected five plants for 13 quantitative traits. The results indicated that the genotype Nagarjuna shows greater yield among the genotypes. The genetic parameters show high GCV and PCV in grain yield per plant, and according to D2 analysis, the 36 genotypes were grouped into 6 clusters based on Tocher's method of cluster formation. Cluster I is the largest cluster, consisting of 29 genotypes, while Cluster II has 3 genotypes. Cluster III, IV, V, and VI were the smallest, with only a single genotype. The maximum intra-cluster distance was found in cluster II (39.19), followed by cluster I (30.15), and the maximum inter-cluster distance was shown in between cluster VI and cluster II (178.97), followed by cluster VI and cluster V (151.75). Based on cluster means, Cluster III (39.67) shows greater among 6 clusters for grain yield per plant as contributing the highest among all the quantitative characters. Hence, these traits could be focused on for selection while improving seed yield and seed quality. On the basis of their greater inter-cluster distance, high value of cluster means, and performance of the individual germplasms for the character, the germplasm could be used in improving seed yield and seed quality programs for improvement of different plant characters of the rice.

Whole-genome Sequencing Association Analysis of Quantitative Platelet Traits in A Large Cohort of β-thalassemia.

Platelet acts as a crucial monitoring indicator for hypercoagulability and thrombosis and a key target for drug regulation. Genotype-phenotype association studies have confirmed that platelet traits are quantitatively regulated by multiple genes. However, there is currently a lack of genetic studies on the heterogeneity of platelet traits in β-thalassemia under hypercoagulable state. Here, we studied the phenotypic heterogeneity of platelet count (PLT) and mean platelet volume (MPV) in 1020 β-thalassemia patients. We further performed a functionally informed whole genome sequencing association analysis of common variants and rare variants (RVs) for PLT and MPV in 916 patients through integrative analysis of whole-genome sequencing data and functional annotation data. Extreme phenotypic heterogeneity of platelet traits was observed in β-thalassemia patients. Additionally, the common variant based gene-level analysis identified the novel gene of RNF144B associated with MPV. The RV analysis identified several novel associations in both coding and noncoding genome, including missense RVs of PPP2R5C associated with PLT and missense RVs of TSSK1B associated with MPV. In conclusion, we performed a comprehensive and systematic whole genome scan of platelet traits in the β-thalassemia cohort, demonstrating the specificity of genetic regulation of platelet traits in the context of β-thalassemia, providing potential targets for intervention.

Inheritance Analysis for Quantitative Traits in F2 Populations of Mustard Genotypes Grown Under Heat Stress Environments

Genetic variability is the basic requirement for improving crops which further leads to progress in crop breeding. This study was carried out to determine the inheritance pattern of various agronomically important traits in F2 populations of mustard genotypes. The objective of this study was to determine the genetic variability for agro-morphological traits under control conditions (CC) and heat stress environments (HS) and provide the future strategies to improve this important oilseed crop. The experiment was conducted at the Botanical Garden, Sindh Agriculture University, Tandojam. During 2022-23, a total of 27 genotypes including nine parental mustard genotypes and eighteen F2 progenies were grown under control and heat stress conditions. The experiment was laid out in a randomized complete block design with three replications. The analysis of variance for the genotypes, treatments, and F2 progenies revealed significant differences (P≤0.05) in most of the studied characters, highlighting the importance of genetic variations in the evaluated breeding materials of mustard for stress breeding. When estimating heritability for different characters, including seed yield plant-1, it was found that F2 crosses showed varying levels of heritability for different characteristics, ranging from low to moderate and high. This implies that careful selection may be conducted for traits that have low heritability, especially for seed yield.; however, those characters which showed high heritability would be selected at early generation stage to improve the characters.

Exploring Genetic Variability, Trait Associations and Path Coefficient Analysis in Pea (Pisum sativum L.) to Advance Breeding Strategies

The experiment was conducted at seed breeding farm, Department of Plant Breeding and Genetics, College of Agriculture, JNKVV, Jabalpur, Madhya Pradesh, India during the rabi season (November, 2019–April, 2020) to estimate the parameters of genetic variability, assess the correlation among traits, and estimate direct and indirect effects. The ANOVA revealed that the mean sum of squares due to genotypes was highly significant for all the traits. The phenotypic coefficient of variation was higher than the genotypic coefficient of variation for all the characters. High values of phenotypic coefficient of variation and genotypic coefficient of variation were observed for most of the traits, while moderate values of phenotypic coefficient of variation and genotypic coefficient of variation were recorded for 100 seed weight, pod length, days to 50% flowering and days to first flower opening. High heritability with high genetic advance as a % of mean was recorded for most of the traits. Moderate heritability and high genetic advance were recorded for the number of primary branches plant-1, secondary branches plant-1 and pod length, indicating the control of additive gene action. Meanwhile, high heritability with moderate genetic advance for days to maturity showed non-additive gene action. Correlation coefficients and path analysis for phenological and quantitative traits indicated that the most important traits are number of seeds plant-1, number of effective pods plant-1, biological yield plant-1 and harvest index. Hence, directional selection through these traits may effectively improve seed yield and its attributes.

Study on correlation and path coefficient analysis for certain quantitative traits in cucumber (Cucumis sativus L.)

Study on correlation and path coefficient analysis for certain quantitative traits in cucumber (Cucumis sativus L.)

Study of Metroglyph Analysis in Faba Bean (Vicia faba L.) Genotypes for Different Quantitative Characters

The study conducted at the Research Farm of Genetics and Plant Breeding, Naini Agricultural Institute, Sam Higginbottom University of Agriculture, Technology and Sciences during the rabi/winter season of 2022-23 aimed to estimate the genetic diversity and morphological variations among 20 Faba bean (Vicia faba L.) genotypes using Anderson’s metroglyph analysis for different quantitative traits. Analysis of variance revealed significant differences for all the characters studied indicating the presence of considerable amount of variability among the genotypes. The genotypes viz, IVT HB19-14 I, IVT HB 19-11, ABSPS-2-1, AVT I HB16-15, IVT HB18-15, VIKRANT (CHECK), ABSPS-1-5, ABSPS-1-2 recorded significantly superior seed yield and yield contributing traits respectively. Six distinct morphological complexes were identified as a result of the analysis, which showed significant variation among the genotypes for the majority of traits. Complex I included eight genotypes with high seed yield and a high number of seeds per plant, while Complex II comprised five genotypes with low seed yield and a low number of seeds per plant. Complex III: High seed yield with a lower number of seeds per plant including three genotypes. Complex IV: Moderate seed yield with a higher number of seeds per plant, represented by two genotypes, Complex V: Very low seed yield and a very low number of seeds per plant, represented by one genotype and Complex VI: Low plant height with a very low number of spikelet’s per panicle, represented by one genotype. The genotypes IVT HB18-15, IVT HB19-13, IVT HB19-14 I, IVT HB19-11, ABSPS-1-1, ABSPS-1-2, ABSPS-1-4, and VIKRANT were identified as superior due to their high index scores and were suggested for use in breeding programs to enhance yield and other desirable traits. The study concluded that metroglyph analysis is an effective method for assessing genetic diversity and morphologicalvariations, providing valuable insights for breeders to improve Faba bean yield and adaptability through targeted cross-breeding of superior genotypes.

MTML: An Efficient Multitrait Multilocus GWAS Method Based on the Cauchy Combination Test.

Genome-wide association study (GWAS) by measuring the joint effect of multiple loci on multiple traits, has recently attracted interest, due to the decreased costs of high-throughput genotyping and phenotyping technologies. Previous studies mainly focused on either multilocus models that identify associations with a single trait or multitrait models that scan a single marker at a time. Since these types of models cannot fully utilize the association information, the powers of the tests are usually low. To potentially address this problem, we present here a multitrait multilocus (MTML) modeling framework that implements in three steps: (1) simplify the complex calculation; (2) reduce the model dimension; (3) integrate the joint contribution of single markers to multiple traits by Cauchy combination. The performances of MTML are evaluated and compared with other three published methods by Monte Carlo simulations. Simulation results show that MTML is more powerful for quantitative trait nucleotide detection and robust for various numbers of traits. In the meanwhile, MTML can effectively control type I error rate at a reasonable level. Real data analysis of Arabidopsis thaliana shows that MTML identifies more pleiotropic genetic associations. Therefore, we conclude that MTML is an efficient GWAS method for joint analysis of multiple quantitative traits. The R package MTML, which facilitates the implementation of the proposed method, is publicly available on GitHub https://github.com/Guohongping/MTML.

Buffalo Selection in Bali Province, Indonesia: Performance and Quantitative Trait Analysis

Buffalo Selection in Bali Province, Indonesia: Performance and Quantitative Trait Analysis

Genome-wide association study, combined with bulk segregant analysis, identify plant receptors and defense related genes as candidate genes for downy mildew resistance in quinoa

BackgroundDowny mildew is the most relevant disease of quinoa and the most widespread. Though, little is known about the genetics of resistance to this disease. The objective of this study was to identify the genomic regions controlling downy mildew resistance in quinoa and candidate genes for this trait. With this aim we carried out a GWAS analysis in a collection formed by 211 quinoa accessions from different origins. This approach was combined with inheritance studies and Bulk Segregant Analysis (BSA) in a segregating population.ResultsGWAS analysis identified 26 genomic regions associated with the trait. Inheritance studies in a F2 population segregating for resistance revealed the existence of a major single dominant gene controlling downy mildew complete resistance in quinoa accession PI614911. Through BSA, this gene was found to be located in chromosome 4, in a region also identified by GWAS. Furthermore, several plant receptors and resistance genes were found to be located into the genomic regions identified by GWAS and are postulated as candidate genes for resistance.ConclusionsUntil now, little was known about the genetic control of downy mildew resistance in quinoa. A previous inheritance study suggested that resistance to this disease was a quantitative polygenic trait and previous GWAS analyses were unable to identify accurate markers for this disease. In our study we demonstrate the existence of, at least, one major gene conferring resistance to this disease, identify the genomic regions involved in the trait and provide plausible candidate genes involved in defense. Therefore, this study significantly increases our knowledge about the genetics of downy mildew resistance and provides relevant information for breeding for this important trait.

Exploring potato diversity: A comprehensive genetic and phenotypic analysis of quantitative and qualitative traits

Exploring potato diversity: A comprehensive genetic and phenotypic analysis of quantitative and qualitative traits

Germline genetic regulation of the colorectal tumor immune microenvironment

ObjectiveTo evaluate the contribution of germline genetics to regulating the briskness and diversity of T cell responses in CRC, we conducted a genome-wide association study to examine the associations between germline genetic variation and quantitative measures of T cell landscapes in 2,876 colorectal tumors from participants in the Molecular Epidemiology of Colorectal Cancer Study (MECC).MethodsGermline DNA samples were genotyped and imputed using genome-wide arrays. Tumor DNA samples were extracted from paraffin blocks, and T cell receptor clonality and abundance were quantified by immunoSEQ (Adaptive Biotechnologies, Seattle, WA). Tumor infiltrating lymphocytes per high powered field (TILs/hpf) were scored by a gastrointestinal pathologist. Regression models were used to evaluate the associations between each variant and the three T-cell features, adjusting for sex, age, genotyping platform, and global ancestry. Three independent datasets were used for replication.ResultsWe identified a SNP (rs4918567) near RBM20 associated with clonality at a genome-wide significant threshold of 5 × 10− 8, with a consistent direction of association in both discovery and replication datasets. Expression quantitative trait (eQTL) analyses and in silico functional annotation for these loci provided insights into potential functional roles, including a statistically significant eQTL between the T allele at rs4918567 and higher expression of ADRA2A (P = 0.012) in healthy colon mucosa.ConclusionsOur study suggests that germline genetic variation is associated with the quantity and diversity of adaptive immune responses in CRC. Further studies are warranted to replicate these findings in additional samples and to investigate functional genomic mechanisms.

Morphological Characterization of Kage and Baruwal Sheep (Ovis aries Linnaeus, 1758) Breeds in Nepal

Sheep farming in Nepal is closely linked to its agricultural heritage and contributes to livelihoods and the socio-economic fabric. This study synthesizes the morphological characterization of Kage and Baruwal (Ovis aries Linnaeus, 1758) sheep, highlighting their genetic and functional attributes, including body size, conformation, coat color, horn morphology, and reproductive parameters. This study synthesizes the morphological characterization of Kage and Baruwal (O. aries) sheep, highlighting their genetic and functional attributes, including body size, conformation, coat color, horn morphology, and reproductive parameters. The analysis revealed a significant difference (P ≤ 0.01**) in quantitative traits between the two breeds. The Baruwal sheep exhibited higher mean values for tail length (12.96 ± 0.47 cm), ear length (10.67±0.20 cm), neck length (21.75±0.38 cm), chest girth (67.14±0.50), height at hip bone (64.78±0.44 cm), body weight (33.04±0.65 Kg), and height below withers (67.10±0.56). Additionally, correlation analysis of different quantitative traits was found to be significant at the 0.01 level on a two-tailed test. The study's results indicate significant quantitative variations, which suggest genetic adaptations and selective pressures. The analysis of qualitative traits highlights differences in horn presence, shape, fleece, head color, neckline, and tail shape, providing insights into genetic diversity and functional adaptations. The study concludes that comprehending such phenotypic traits helps with breed management, conservation, and sustainable agriculture. The preservation of genetic diversity and adaptability is underscored by indigenous sheep breeds, which requires further research to elucidate the genetic mechanisms underlying these traits.

Morphological diversity analysis for quantitative traits in Quality Protein maize (QPM)

Morphological diversity analysis for quantitative traits in Quality Protein maize (QPM)

Genetic analysis of quantitative traits in Blackgram using line x tester design

Genetic analysis of quantitative traits in Blackgram using line x tester design

Genotype Selection from Azide‐Induced Rice Mutants Using Multitrait Genotype–Ideotype Distance Index (MGIDI): Unveiling Promising Variants for Yield Improvement

Development of high‐yielding rice (Oryza sativa L.) is a crucial need for succeeding food security that needs the presence of great genetic variability to be used in breeding programs. Creating new variants through sodium azide mutagenesis can be a better alternative in advancing plant breeding issues. The generation and characterization of mutants represent an effective method for choosing genotypes with desired attributes. In this study, we focused on inducing mutations in the genetic base of a mega rice variety (BRRI dhan28) using sodium azide, evaluating the genetic diversity of the mutants, and identifying promising genotypes among the mutants using quantitative trait analysis and genetic criteria. The mutants exhibited substantial variation, as evidenced by descriptive statistics and analysis of variance. The estimated heritability and genetic advance indicated that nearly all traits had a high level of heritability and followed a complex pattern of inheritance. The strong correlations observed between grain yield and flag leaf length, branch panicle−1, grain panicle−1, 100‐grain weight, straw yield hill−1, and harvest index indicate that prioritizing these traits during selection could substantially improve other desirable characteristics. Additionally, we employed the principal component analysis which revealed that the first two components collectively accounted for 32.16% of the total variation, providing essential information about the genetic relatedness of the mutants. The Multitrait Genotype–Ideotype Distance Index (MGIDI) analysis revealed that out of 100 mutants, only eight exhibited noteworthy performance. These findings provide insights into the efficiency of azide in creating genetic variations in rice traits and offer valuable resources for future breeding programs aimed at developing high‐performing rice varieties.

Exploring genetic diversity in traditional rice genotypes (Oryza sativa L.) through cluster analysis of qualitative and quantitative traits

Exploring genetic diversity in traditional rice genotypes (Oryza sativa L.) through cluster analysis of qualitative and quantitative traits

Studies on character association and path coefficient analysis for various qualitative and quantitative traits in bottle gourd (Lagenaria siceraria (Mol.) Standl.)

Studies on character association and path coefficient analysis for various qualitative and quantitative traits in bottle gourd (Lagenaria siceraria (Mol.) Standl.)

Correlation and path analysis for quantitative traits in greengram

Correlation and path analysis for quantitative traits in greengram