scholarly journals Genetic Diversity among Selected Medicago sativa Cultivars Using Inter-Retrotransposon-Amplified Polymorphism, Chloroplast DNA Barcodes and Morpho-Agronomic Trait Analyses

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 995
Author(s):  
Abdelfattah Badr ◽  
Nahla El-Sherif ◽  
Sara Aly ◽  
Shafik D. Ibrahim ◽  
Mohamed Ibrahim
Keyword(s):  
Genetic Diversity ◽  
Medicago Sativa ◽  
Chloroplast Dna ◽  
Genetic Relatedness ◽  
Agronomic Traits ◽  
Principal Component ◽  
Dna Barcodes ◽  
Breeding Lines ◽  
Molecular Approaches ◽  
High Forage

Alfalfa (Medicago sativa L.) is a major forage crop of family Fabaceae and is frequently cultivated in Egypt. The present study is concerned with the genetic discrimination of fifteen alfalfa cultivars from three different countries (Egypt, Australia, and USA) using two molecular approaches: inter-retrotransposon-amplified polymorphism (IRAP) markers and two chloroplast DNA barcodes matK and the trnH in addition to the analysis of fifteen morpho-agronomic traits. The genetic relatedness, based on analysis of IRAP marker polymorphism and produced using eleven primers by clustering via principal component analysis (PCA) and multivariate heatmap biostatistical methods differentiated the two Egyptian cultivars EGY1-Ismailia1 and EGY2-Nubaria1 from the three Australian and seven American cultivars, with some distinction of the cv. USA6-SW9720 and cv. AUS4-SuperFast. The results were also supported by the sequence analysis of the matK and the trnH genes on the genetic relatedness between eight cultivars. Moreover, it might be suggested that breeding lines from M. sativa cultivars may provide novel insights and a better understanding of the domestication of M. sativa genetic diversity. The classification of the eight cultivars, as revealed by morpho-agronomic traits, confirmed the close genetic relationship between the two Egyptian cultivars and indicated some resemblance between them and the AUS2-Siri Nafa, whereas the two American cultivars, USA1-Super supreme and USA4-Cuf101, were clearly isolated from a cluster of other three cultivars USA7-SW9628, USA8-Magna901, and USA9-Perfect. The results are useful sources of genetic information for future breeding programs in crop development and open new possibilities of producing M. sativa lines harboring high forage quality, productivity, and resistance to biotic and abiotic stresses.

scholarly journals Assessment of wild tomato accessions for fruit yield, physicochemical and nutritional properties under a rain forest agro-ecology

2020 ◽  
Vol 1 (2) ◽  
pp. 1-11
Author(s):  
Dorcas Ibitoye ◽  
Adesike Kolawole ◽  
Roseline Feyisola
Keyword(s):  
Rain Forest ◽  
Agronomic Traits ◽  
Block Design ◽  
Principal Component ◽  
Fruit Yield ◽  
Soluble Solids ◽  
Forest Zone ◽  
Breeding Lines ◽  
Wild Tomato ◽  
Solanum Lycopersicum L

Tomato (Solanum lycopersicum L.) is a broadly consumed fruit vegetable globally. It is one of the research mandate vegetable of the National Horticultural Research Institute (NIHORT), Ibadan, Nigeria. The institute’s contains diverse collections of tomato accessions and wild relatives, without utilization information for the African continent. With the decline in diversity and potential of cultivars, a robust tomato breeding pipeline with broad genetic base that eliminates redundancy in the development of lines with desired horticultural traits is paramount. This study evaluated the mean performance and variations of thirteen wild tomato accessions obtained from the C.M. Rick Tomato Genetic Resource Center, University of California, Davis, USA, evaluated for agronomic, nutritional and physicochemical traits under a rain forest zone in Nigeria. The accessions were planted and grown in three replications with randomized complete block design. Agronomic traits, physicochemical and nutritional parameters were measured and analyzed. There was significant (P < 0.001) variation among accessions for all traits measured. Accession LA0130 was separated from others by cluster analysis and was outstanding for its unique attributes which include: fruit yield parameters, total soluble solids, acidity and content. The principal component analysis suggests fruit yield related traits, acidity and contributed most to the variation among the 13 accessions. The results obtained can be used to breed materials adapted to a rain forest . These wild tomato accessions have genes with desirable agronomic, nutritional and physicochemical traits that could be into breeding lines to improve commercial tomato varieties.

scholarly journals Genetic Diversity of Agronomic Traits in Advanced Breeding Lines of Rice (Oryza Sativa)

2019 ◽  
Vol 11 (30) ◽  
pp. 178-187
Author(s):  
Alireza Nabipour ◽  
Mohammad Norouzi ◽  
◽  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Agronomic Traits ◽  
Breeding Lines

scholarly journals Genetic diversity of physical, nutritional and functional properties of cowpea grain and relationships among the traits

2015 ◽  
Vol 14 (1) ◽  
pp. 67-76 ◽  
Author(s):  
Satoru Muranaka ◽  
Mariko Shono ◽  
Takao Myoda ◽  
Junko Takeuchi ◽  
Jorge Franco ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Crude Protein ◽  
Agronomic Traits ◽  
Sub Saharan Africa ◽  
Small Scale ◽  
Cash Income ◽  
Breeding Lines ◽  
Nutrient Contents ◽  
Sub Saharan ◽  
Small Scale Farmers

Cowpea is traditionally important as an affordable source of protein and minerals and of cash income in sub-Saharan Africa, especially for small-scale farmers who have limited options for food and cash crops. The development and deployment of cowpea varieties with improved nutrition and quality that meet the needs of farmers and consumers should enhance cowpea consumption and production in the region. We have identified genetic diversity in various grain quality-related traits of cowpea and relationships among the traits. Wide genetic variation and strong correlations among crude protein, Fe and Zn contents suggest the possibility of improving the concentrations of these nutritional factors simultaneously. Low associations among physical and nutritional properties of grain indicate the possibility of introgressing favorable traits utilizing identified genetic resources. However, narrow variation in amino acid (AA) composition suggests a lesser possibility of improving the contents of specific AAs in cowpea, but it gave a reliable nitrogen-to-protein conversion factor of 5.45 for the estimation of crude protein content. Several improved breeding lines were identified with low concentrations of flatulence-causing oligosaccharides and various favorable agronomic traits and nutrient contents. TVu-12802 had the highest contents of crude protein and high contents of micronutrients, with a low ratio of phytic acid to Fe and Zn contents.

scholarly journals Genetic divergence of Nigerian and Indian pearl millet accessions based on agronomical and morphological traits

2017 ◽  
Vol 62 (2) ◽  
pp. 115-131
Author(s):  
David Animasaun ◽  
Joseph Morakinyo ◽  
Rama Krishnamurthy ◽  
Oba Mustapha
Keyword(s):  
Plant Height ◽  
Pearl Millet ◽  
Morphological Traits ◽  
Genetic Relatedness ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Principal Component ◽  
Leaf Length ◽  
Leaf Width ◽  
Number Of Leaves

The study assessed the genetic diversity of pearl millet accessions grown in Nigeria and India based on morpho-agronomic traits in order to identify genotypes with superior characters which could be utilized in breeding programmes. Twenty-four pearl millet accessions were grown and evaluated for agronomic and morphological traits during the dry and wet seasons of 2015-2016. Data collected on the accessions using standard descriptors were analysed statistically. IP22281 had the highest mean plant height (108.90 cm) while NGB00531 recorded the lowest (61.02 cm). Significant intra-specific variation existed in number of leaves per plant, leaf length, leaf width, number of nodes and internode length, however, stem girth was similar for the accessions. Tillering was generally poor with the highest value (1.60 tillers per plant) found in NGB00531. A significant positive correlation occurred between plant height, number of leaves, leaf length and leaf width. Panicles emerged between 44 and 56 days and NGB00548 had the shortest maturity time. Also, panicle length and peduncle diameter varied significantly for the accessions. The highest grain yield and 1000-grain weight were recorded in NGB00616 and the lowest yield and weight were recorded in IP22269. The principal component analysis grouped the accessions into four clusters, comprising mixtures of Nigerian and Indian members. Similarly, the dendrogram grouped the accessions into two main groups which were sub-divided into smaller clusters with accessions from Nigeria and India in the same cluster. The study concludes that variations in morpho-agronomic and yield characters among the accessions studied could be harnessed for crop improvement. The clustering pattern of these accessions indicated their genetic relatedness, possibly from the same progenitor, but separation by geographical or ecological isolation mechanisms.

scholarly journals Genetic diversity and GWAS of agronomic traits using an ICARDA lentil (Lens culinaris Medik.) Reference Plus collection

2021 ◽  
pp. 1-10
Author(s):  
Karthika Rajendran ◽  
Clarice J. Coyne ◽  
Ping Zheng ◽  
Gopesh Saha ◽  
Dorrie Main ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Lens Culinaris ◽  
Agronomic Traits ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Phenotypic Data ◽  
Reference Set ◽  
Genome Wide

Abstract Genotyping of lentil plant genetic resources holds the promise to increase the identification and utilization of useful genetic diversity for crop improvement. The International Center for Agriculture Research in the Dry Areas (ICARDA) lentil reference set plus collection of 176 accessions was genotyped using genotyping-by-sequencing (GBS) and 22,555 SNPs were identified. The population structure was investigated using Bayesian analysis (STRUCTURE, k = 3) and principal component analysis. The two methods are in concordance. Genome-wide association analysis (GWAS) using the filtered SNP set and ICARDA historical phenotypic data discovered putative markers for several agronomic traits including days to first flower, seeds per pod, seed weight and days to maturity. The genetic and genomic resources developed and utilized in this study are available to the research community interested in exploring the ICARDA reference set plus collection using GWAS.

scholarly journals Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli (Brassica oleracea L. var. italica) in China

2021 ◽  
Vol 12 ◽  
Author(s):  
Yusen Shen ◽  
Jiansheng Wang ◽  
Ranjan K. Shaw ◽  
Huifang Yu ◽  
Xiaoguang Sheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Oleracea ◽  
Structure Analysis ◽  
Genetic Relatedness ◽  
Gene Diversity ◽  
Principal Component ◽  
Resolving Power ◽  
Limited Information ◽  
Large Collection

Broccoli (Brassica oleracea var. italica) is one of the most important and nutritious vegetables widely cultivated in China. In the recent four decades, several improved varieties were bred and developed by Chinese breeders. However, the efforts for improvement of broccoli are hindered by limited information of genetic diversity and genetic relatedness contained within the available germplasms. This study evaluated the genetic diversity, genetic relationship, population structure, and fingerprinting of 372 accessions of broccoli representing most of the variability of broccoli in China. Millions of SNPs were identified by whole-genome sequencing of 23 representative broccoli genotypes. Through several stringent selection criteria, a total of 1,167 SNPs were selected to characterize genetic diversity and population structure. Of these markers, 1,067 SNPs were genotyped by target sequencing (GBTS), and 100 SNPs were genotyped by kompetitive allele specific PCR (KASP) assay. The average polymorphism information content (PIC) and expected heterozygosity (gene diversity) values were 0.33 and 0.42, respectively. Diversity analysis revealed the prevalence of low to moderate genetic diversity in the broccoli accessions indicating a narrow genetic base. Phylogenetic and principal component analyses revealed that the 372 accessions could be clustered into two main groups but with weak groupings. STRUCTURE analysis also suggested the presence of two subpopulations with weak genetic structure. Analysis of molecular variance (AMOVA) identified 13% variance among populations and 87% within populations revealing very low population differentiation, which could be attributed to massive gene flow and the reproductive biology of the crop. Based on high resolving power, a set of 28 KASP markers was chosen for DNA fingerprinting of the broccoli accessions for seed authentication and varietal identification. To the best of our knowledge, this is the first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli. This work broadens the understanding of diversity, phylogeny, and population structure of a large collection of broccoli, which may enhance future breeding efforts to achieve higher productivity.

scholarly journals Genetic Variability of Maize Hybrids and Populations and Interrelationships among Grain Yield and Its Related Traits under Drought and Low N Using Multivariate Analysis

2020 ◽  
pp. 26-44 ◽  
Author(s):  
A. M. M. Al- Naggar ◽  
M. M. Shafik ◽  
Rabeh Y. M. Musa ◽  
A. S. M. Younis ◽  
A. H. Anany
Keyword(s):  
Genetic Diversity ◽  
Multivariate Analysis ◽  
Grain Yield ◽  
Genetic Relatedness ◽  
Agronomic Traits ◽  
Chlorophyll Concentration ◽  
Kernel Weight ◽  
Phenotypic Data ◽  
Germplasm Collections ◽  
Maize Genotypes

One of the best biometrical methods for estimating genetic diversity among germplasm collections is multivariate analysis; it is used to study their variability and genetic relatedness in order to increase their value in plant breeding programs. The objectives of the present study were to: (i) evaluate the magnitude of genetic diversity, based on phenotypic data, among 19 maize genotypes, under drought and/or low N stressed conditions in the field, using principle component analysis (PCA) and (ii) assess the interrelationships between maize grain yield and its related traits under such stressed conditions using genotype × trait (GT) biplot analysis. An experiment was conducted in two seasons using a split-split plot design with 3 replications, where 2 irrigation regimes (well-watered and water stressed at flowering) occupied the main plots, three N rates (high N, medium N and low N) occupied the sub plots and 19 maize genotypes occupied the sub-sub plots. The genotypes were evaluated for 19 agronomic traits. Analysis of variance was performed under each of the six environments. Significant differences (p≤0.01) were recorded among the maize genotypes for all studied traits under each environment. The best genotypes for each trait were identified. Results of the GT biplot indicated that high means of 100-kernel weight (100-KW), ears/plant (EPP), ear height, days to silking, days to anthesis, plant height, and chlorophyll concentration index (CCI) under water stress (WS), kernels/row (KPR), EPP, 100-KW and CCI under low N and KPR, EPP and 100-KW under WS combined with low N environment and low values of anthesis-silking interval (ASI) under the three stressed environments could be considered selection criteria for high grain yield under respective stressed environments and for drought and/or low N tolerance. It is recommended to select for high values of KPR, EPP and 100-KW and low value of ASI in order to increase grain yield under such stressed conditions.

scholarly journals Genome-level diversification of eight ancient tea populations in the Guizhou and Yunnan regions identifies candidate genes for core agronomic traits

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Litang Lu ◽  
Hufang Chen ◽  
Xiaojing Wang ◽  
Yichen Zhao ◽  
Xinzhuan Yao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Agronomic Traits ◽  
Association Studies ◽  
Functional Characterization ◽  
Principal Component ◽  
Tea Plant ◽  
Guizhou Province ◽  
Genome Wide Association Studies ◽  
Tea Plants

AbstractThe ancient tea plant, as a precious natural resource and source of tea plant genetic diversity, is of great value for studying the evolutionary mechanism, diversification, and domestication of plants. The overall genetic diversity among ancient tea plants and the genetic changes that occurred during natural selection remain poorly understood. Here, we report the genome resequencing of eight different groups consisting of 120 ancient tea plants: six groups from Guizhou Province and two groups from Yunnan Province. Based on the 8,082,370 identified high-quality SNPs, we constructed phylogenetic relationships, assessed population structure, and performed genome-wide association studies (GWAS). Our phylogenetic analysis showed that the 120 ancient tea plants were mainly clustered into three groups and five single branches, which is consistent with the results of principal component analysis (PCA). Ancient tea plants were further divided into seven subpopulations based on genetic structure analysis. Moreover, it was found that the variation in ancient tea plants was not reduced by pressure from the external natural environment or artificial breeding (nonsynonymous/synonymous = 1.05). By integrating GWAS, selection signals, and gene function prediction, four candidate genes were significantly associated with three leaf traits, and two candidate genes were significantly associated with plant type. These candidate genes can be used for further functional characterization and genetic improvement of tea plants.

scholarly journals Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Heshan Du ◽  
Jingjing Yang ◽  
Bin Chen ◽  
Xiaofen Zhang ◽  
Jian Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relatedness ◽  
Principal Component ◽  
Shape Index ◽  
Fruit Shape ◽  
Snp Markers ◽  
Variety Identification ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Multiplex Amplification

Abstract Background The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index (p < 0.0001). Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.

Sign in / Sign up

Export Citation Format

Share Document