Rendering Multivariate Statistical Models for Genetic Diversity Assessment in a A-Genome Diploid Wheat Population

Diversifying available natural resources to cope with abrupt climatic changes and the necessity to equalize rising agricultural production with improved ability to endure environmental influence is the dire need of the day. Inherent allelic variability regarding significant economic traits featuring both enhanced productivity and environmental adaptability is one such prominent need. To address this requirement, a series of analyses were conducted in this study for exploring natural diploid wheat germplasm resources. The current study involved 98 Recombinant Inbred Lines (RILs) populations developed by crossing two diploid ‘A’ sub-genome wheat species, Triticummonococcum and Triticum boeoticum, enriched with valuable alleles controlling, in particular, biotic and abiotic stresses tolerance. Their 12 phenotypic traits were explored to reveal germplasm value. All traits exhibited vast diversity among parents and RILs via multivariate analysis. Most of the investigated traits depicted significant (p < 0.05) positive correlations enlightening spikelet per spike, total biomass, seed weight per spike, number of seeds per spike, plant height, and days to heading as considerably focused traits for improving hexaploid wheat. Principal component analysis (PCA) exhibited 61.513% of total variation with three PCs for 12 traits. Clustering of genotypes happened in three clades, and the two parents were separated into two extreme clusters, validating their enrichment of diversity. This study provided beneficial aspects of parental resources rich in diverse alleles. They can be efficiently exploited in wheat improvement programs focusing on introgression breeding and the recovery of eroded genetic factors in currently available commercial wheat cultivars to sustain calamities of environmental fluctuations.

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ESTIMATION OF GENETIC DIVERGENCE IN CHILLI PEPPER (CAPSICUM ANNUUM L.) GENOTYPES FOR MORPHOLOGICAL AND FRUIT TRAITS UNDER HOT CLIMATE OF UMERKOT, SINDH

Pakistan Journal of Agriculture, Agricultural Engineering and Veterinary Sciences ◽

10.47432/2021.37.1.3 ◽

2021 ◽

Vol 37 (1) ◽

pp. 21-28

Author(s):

A. Memon ◽

R. Ahmad ◽

M. S. Depar ◽

A. K. Pathan ◽

D. Ibrar

Keyword(s):

Cluster Analysis ◽

Genetic Divergence ◽

Agricultural Research ◽

Arid Zone ◽

Principal Component ◽

Fruit Weight ◽

Economic Traits ◽

Chilli Pepper ◽

Hot Climate ◽

Improvement Programs

Thirty-two genotypes of chilli from three different sources (local dandicuts, AVRDC and PGRI PARC) were evaluated for the presence of genetic divergence among them for different agro-economic traits i.e., plant height, stem girth, fruit length, fruit girth, number of fruits per plant, number of seed per fruit, fresh fruit weight and dry fruit weight at Arid Zone Agricultural Research Institute, Umerkot, Sindh during 2018. All these genotypes were found to be significantly different from each other for all the studied traits. For further diversity analysis, multivariate analyses like principal component analysis (PCA) and Cluster analysis were also performed to figure out the traits responsible for maximum variability and grouping of genotypes according to their similarities and differences for their future utilization in chilli breeding programs. PCA analysis showed that first four PCs exhibited 82.79% of the total variability among these 32 chilli genotypes. Cluster analysis showed four different sub-clusters and the genotypes from every single source merge in each sub-cluster, thus showing that chilli genotypes are from different geographical backgrounds. Based on these results, the chilli genotypes can be further utilized in future chilli improvement programs in Pakistan. Genotypes AZRI-DS-14, AZRI-DS-01 and AVPP-9804 showed better performance.

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Quantitative Epigenetics: A New Avenue for Crop Improvement

Epigenomes ◽

10.3390/epigenomes4040025 ◽

2020 ◽

Vol 4 (4) ◽

pp. 25 ◽

Cited By ~ 1

Author(s):

Vijay Gahlaut ◽

Gaurav Zinta ◽

Vandana Jaiswal ◽

Sanjay Kumar

Keyword(s):

Molecular Breeding ◽

Recombinant Inbred Lines ◽

Crop Improvement ◽

Genotyping By Sequencing ◽

Phenotypic Traits ◽

Epigenetic Variation ◽

Epigenome Editing ◽

Epigenetic Diversity ◽

Improvement Programs

Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Furthermore, the development of epigenetic recombinant inbred lines (epi-RILs) in model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Likewise, epigenome-wide association study (EWAS) and epi-genotyping by sequencing (epi-GBS) have revolutionized the field of epigenetics research in plants. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can potentially facilitate epigenetic based molecular breeding of important crop plants.

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Genome-Wide Association Study for Plant Architecture and Bioenergy Traits in Diverse Sorghum and Sudangrass Germplasm

Agronomy ◽

10.3390/agronomy10101602 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1602

Author(s):

Feng Luo ◽

Zhongyou Pei ◽

Xiongwei Zhao ◽

Huifen Liu ◽

Yiwei Jiang ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Sweet Sorghum ◽

Plant Architecture ◽

Genome Wide Association Study ◽

Recombinant Inbred Lines ◽

Genome Wide Association ◽

Phenotypic Traits ◽

Genome Wide ◽

A Genome

Sorghum is an important grain, forage, and bioenergy crop. The objective of this study was to identify genetic signals associated with plant architecture and bioenergy traits in sorghum and sudangrass germplasm through a genome-wide association study (GWAS). Plant height (HT), tiller number (TN), internode number (IN), stem diameter (SD), panicle length (PL), panicle weight (PW), reducing sugar (RS) content, Brix, and protein (PRO) content were assessed in 300 germplasm consisting of grain sorghum, sweet sorghum, sudangrass, sweet sorghum-sweet sorghum recombinant inbred lines (RILs) and sudangrass-sudangrass RILs grown in three different environments over two years. Large variations of phenotypic traits were observed in the population panel. The heritability of traits were all higher than 0.5, ranging from 0.52 (PRO) to 0.92 (HT) with an average of 0.76. The population exhibited three population structures (Q) and minor relative kinship (K), assessed by using 7982 single-nucleotide polymorphisms (SNPs). After controlling Q and K, GWAS identified 24 SNPs that were significantly associated with traits, including three SNPs with HT, four with TN, four with PL, three with Brix, and ten with RS. Of them, seven SNPs were novel signals that were not identified previously, including one for HT, one for TN, one for Brix, and four for RS. The putative candidate genes involved in brassinosteroid regulatory pathway, auxin biosynthesis, carbohydrate metabolism, and sugar transport were identified underlying the significant SNPs. Identification of SNP signals and related candidate genes would enrich the current genomic resource for further molecular breeding aimed at improvement of food, feed, and biofuel productions of sorghum.

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Phenotypic characterization and principal component analyses of indigenous chicken breeds in Indonesia

Veterinary World ◽

10.14202/vetworld.2021.1665-1676 ◽

2021 ◽

pp. 1665-1676

Author(s):

Dyah Maharani ◽

Fatmawati Mustofa ◽

Aprilianna Putri Z. N. L. Sari ◽

Akhmad Fathoni ◽

Heru Sasongko ◽

...

Keyword(s):

Phenotypic Variation ◽

Quantitative Traits ◽

Principal Component ◽

Phenotypic Characterization ◽

Phenotypic Traits ◽

Indigenous Chicken ◽

Mean Values ◽

Indigenous Chickens ◽

Chicken Breeds ◽

Improvement Programs

Background and Aim: Understanding the phenotypic characteristics of indigenous livestock breeds is essential for their utilization and conservation. This study aimed to characterize indigenous chicken breeds in Indonesia based on phenotypic traits. Materials and Methods: Data on eight qualitative and 12 quantitative traits were recorded for 250 chickens from six breeds: Black Kedu, Gaga, Merawang, Nunukan, Pelung, and Sentul. Data were analyzed using descriptive statistics and one-way analysis of variance to test the effect of breed on observed traits. Moreover, principal component analysis (PCA) was conducted separately for each chicken breed. Data on quantitative traits were subjected to Kaiser-Meyer-Olkin, which was computed to test the sampling adequacy and the pattern of correlation among the traits, and Bathlett's tests were used to assess the validity of the factor analysis of each of the datasets and determine whether the partial correlations among traits were small. Results: We found considerable phenotypic variation in both qualitative and quantitative traits among indigenous chicken breeds. Multicolored plumage (96.40%), wild plumage (39.20%), gold feather flick (51.20%), yellow shank (36.80%), single comb (80.80%), red comb (94.80%), red earlobe (77.60%), and orange eyes (61.60%) were the most common features in the indigenous chickens. In addition, breed had a significant effect on all the quantitative traits that were analyzed (p<0.05). There were higher mean values for all quantitative traits for Pelung chickens than other chickens. In addition, the overall mean values for all quantitative traits in Merawang chicken were intermediate between Pelung chickens and Black Kedu, Gaga, and Nunukan chickens. The PCA showed two principal factors extracted that accounted for 77.80% and 78.38% of the total variance in the original variables for males and females, respectively. Conclusion: In general, body weight and body measurements, except wattle length, were loaded in PC1 as the primary factors responsible for the variation. The phenotypic variation observed in indigenous chickens in Indonesia could provide valuable basic information for the design of selection and genetic improvement programs.

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Quantitative Epigenetics: A New Avenue for Crop Improvement

10.20944/preprints202009.0348.v1 ◽

2020 ◽

Author(s):

Vijay Gahlaut ◽

Gaurav Zinta ◽

Vandana Jaiswal

Keyword(s):

Molecular Breeding ◽

Recombinant Inbred Lines ◽

Crop Improvement ◽

Phenotypic Traits ◽

Epigenetic Variation ◽

Model Species ◽

Epigenome Editing ◽

Epigenetic Diversity ◽

Improvement Programs

Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Further, the development of epigenetic recombinant inbred lines (epi-RILs) in the model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can facilitate epigenetic based molecular breeding of important crop plants.

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Quantitative Epigenetics: A New Avenue for Crop Improvement

10.20944/preprints202009.0348.v2 ◽

2020 ◽

Author(s):

Vijay Gahlaut ◽

Gaurav Zinta ◽

Vandana Jaiswal ◽

Sanjay Kumar

Keyword(s):

Molecular Breeding ◽

Recombinant Inbred Lines ◽

Crop Improvement ◽

Phenotypic Traits ◽

Epigenetic Variation ◽

Model Species ◽

Epigenome Editing ◽

Epigenetic Diversity ◽

Improvement Programs

Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Further, the development of epigenetic recombinant inbred lines (epi-RILs) in the model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can facilitate epigenetic based molecular breeding of important crop plants.

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Genetic Evaluation and Bi-plot Analysis in Okra Hybrids for Yield, Quality Components and YVMV Resistance

Journal of AgriSearch ◽

10.21921/jas.5.4.5 ◽

2018 ◽

Vol 5 (04) ◽

Author(s):

SS SOLANKEY ◽

ANIL K SINGH

Keyword(s):

Genetic Divergence ◽

Principal Component ◽

F1 Hybrids ◽

Genetic Advance ◽

Economic Traits ◽

Cross Combination ◽

Plot Analysis ◽

Eigen Value ◽

Coefficient Of Variability ◽

Yield Quality

Fifty one okra F1 hybrids (using 17 lines as female and 3 testers as male parent) were evaluated in RCBD design during two different consecutive seasons (summer and rainy). Phenotypic coefficient of variability (PCV) was higher than genotypic coefficient of variability (GCV) for all studied character exhibiting environmental effects on the expression of characters. Heritability (h2b) along with genetic advance per cent of mean was found highest for character YVMV (86.95% and 150.61%). All the 51 okra hybrids were grouped into 4 distinct clusters in which Cluster II was the largest cluster having 28 F1s (54.90% of total F1s) followed by Cluster I with 14 F1s (27.45% of total F1s). Out of the major 6 PCs, 4 principal components (PC1, PC2, PC3 and PC4) accounted with proportionate values of 22.61, 17.22, 11.87 and 10.63%, respectively and contributed 62.33 % of the cumulative variation having Eigen value more than one. Moreover, based on PCs and genetic divergence in Cluster I and Cluster IV for plant height, YVMV and number of fruit per plant is important to identify the best cross combination (Arka Abhay × Arka Anamika) in okra. Therefore, the best cross combinations for improvement in various economic traits can be recommended on the basis of genetic divergence and principal component analysis in okra.

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Evaluation of indigenous aromatic rice cultivars from sub-Himalayan Terai region of India for nutritional attributes and blast resistance

Scientific Reports ◽

10.1038/s41598-021-83921-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Debayan Mondal ◽

Prudveesh Kantamraju ◽

Susmita Jha ◽

Gadge Sushant Sundarrao ◽

Arpan Bhowmik ◽

...

Keyword(s):

Nutritive Value ◽

Amylose Content ◽

Blast Resistance ◽

Starch Content ◽

Low Cost ◽

Principal Component ◽

Blast Disease ◽

Basmati Rice ◽

Phenotypic Traits ◽

Rice Cultivars

AbstractIndigenous folk rice cultivars often possess remarkable but unrevealed potential in terms of nutritional attributes and biotic stress tolerance. The unique cooking qualities and blissful aroma of many of these landraces make it an attractive low-cost alternative to high priced Basmati rice. Sub-Himalayan Terai region is bestowed with great agrobiodiversity in traditional heirloom rice cultivars. In the present study, ninety-nine folk rice cultivars from these regions were collected, purified and characterized for morphological and yield traits. Based on traditional importance and presence of aroma, thirty-five genotypes were selected and analyzed for genetic diversity using micro-satellite marker system. The genotypes were found to be genetically distinct and of high nutritive value. The resistant starch content, amylose content, glycemic index and antioxidant potential of these genotypes represented wide variability and ‘Kataribhog’, ‘Sadanunia’, ‘Chakhao’ etc. were identified as promising genotypes in terms of different nutritional attributes. These cultivars were screened further for resistance against blast disease in field trials and cultivars like ‘Sadanunia’, ‘T4M-3-5’, ‘Chakhao Sampark’ were found to be highly resistant to the blast disease whereas ‘Kalonunia’, ‘Gobindabhog’, ‘Konkanijoha’ were found to be highly susceptible. Principal Component analysis divided the genotypes in distinct groups for nutritional potential and blast tolerance. The resistant and susceptible genotypes were screened for the presence of the blast resistant pi genes and association analysis was performed with disease tolerance. Finally, a logistic model based on phenotypic traits for prediction of the blast susceptibility of the genotypes is proposed with more than 80% accuracy.

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Codon usage bias and environmental adaptation in microbial organisms

Molecular Genetics and Genomics ◽

10.1007/s00438-021-01771-4 ◽

2021 ◽

Author(s):

Davide Arella ◽

Maddalena Dilucca ◽

Andrea Giansanti

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Pathogenic Bacteria ◽

Large Scale ◽

Synonymous Codon ◽

Principal Component ◽

Gene Copy ◽

Phenotypic Traits ◽

Translational Efficiency ◽

Microbial Organisms

AbstractIn each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism’s lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.

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Quantitative Trait Loci for the Monoamine-Related Traits Heart Rate and Headless Behavior inDrosophila melanogaster

Genetics ◽

10.1093/genetics/157.1.283 ◽

2001 ◽

Vol 157 (1) ◽

pp. 283-294 ◽

Cited By ~ 2

Author(s):

Kristie Ashton ◽

Ana Patricia Wagoner ◽

Roland Carrillo ◽

Greg Gibson

Keyword(s):

Heart Rate ◽

Genetic Variation ◽

Recombinant Inbred Lines ◽

Model Organism ◽

Interval Mapping ◽

Activity Levels ◽

Environmental Variance ◽

Genome Wide ◽

A Genome ◽

Monoamine Receptors

AbstractDrosophila melanogaster appears to be well suited as a model organism for quantitative pharmacogenetic analysis. A genome-wide deficiency screen for haploinsufficient effects on prepupal heart rate identified nine regions of the genome that significantly reduce (five deficiencies) or increase (four deficiencies) heart rate across a range of genetic backgrounds. Candidate genes include several neurotransmitter receptor loci, particularly monoamine receptors, consistent with results of prior pharmacological manipulations of heart rate, as well as genes associated with paralytic phenotypes. Significant genetic variation is also shown to exist for a suite of four autonomic behaviors that are exhibited spontaneously upon decapitation, namely, grooming, grasping, righting, and quivering. Overall activity levels are increased by application of particular concentrations of the drugs octopamine and nicotine, but due to high environmental variance both within and among replicate vials, the significance of genetic variation among wild-type lines for response to the drugs is difficult to establish. An interval mapping design was also used to map two or three QTL for each behavioral trait in a set of recombinant inbred lines derived from the laboratory stocks Oregon-R and 2b.

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