Dataset Information

Genetic Diversity and Population Structure of F_3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

ABSTRACT: The availability of information on the genetic diversity and population structure in wheat (Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F_3:6) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon's information index (I) = 0.494, diversity index (h) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity (I = 0.348, h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars.

SUBMITTER: Eltaher S

PROVIDER: S-EPMC5857551 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Genetic Diversity and Population Structure of F<sub>3:6</sub> Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

Eltaher Shamseldeen S Sallam Ahmed A Belamkar Vikas V Emara Hamdy A HA Nower Ahmed A AA Salem Khaled F M KFM Poland Jesse J Baenziger Peter S PS

Frontiers in genetics 20180312

The availability of information on the genetic diversity and population structure in wheat (<i>Triticum aestivum</i> L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic d ...[more]

PMID: 29593779

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Project description:BackgroundDurum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions.ResultsWe assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000-2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915-1979, 1980-1999 and 2000-2020).ConclusionsOur results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.

Project description:Wheat is one of the most important cereals, whose growth and development is strongly limited by drought. This study investigated the physiological and metabolic response of six winter wheat cultivars to drought with the emphasis on the induction of dominant metabolites affected by the treatment and genotypes or both. The plants were exposed to a moderate (non-lethal) drought stress, which was induced by withholding watering for six days under controlled greenhouse conditions. A decline in CO2 assimilation (Pn) and transpiration rate, stomata closure, a decrease in relative water content (RWC) and increase of malondialdehyde content were observed in drought-treated plants of all cultivars. These changes were most pronounced in Ellvis, while Soissons was able to retain the higher RWC and Pn. Among the studied metabolites, sugars (sucrose, glucose, fructose, several disaccharides), organic acids (malic acid, oxalic acids), amino acids (proline, threonine, gamma-aminobutyric acid (GABA), glutamine) and sugar alcohols such as myo-inositol accumulated to higher levels in the plants exposed to drought stress in comparison with the control. The accumulation of several metabolites in response to drought differed between the genotypes. Drought induced the production of sucrose, malic acid and oxalic acid, unknown organic acid 1, unknown disaccharide 1, 2 and 3, GABA, L-threonine, glutamic acid in four (Soissons, Žitarka, Antonija or Toborzó) out of six genotypes. In addition, Soissons, which was the most drought tolerant genotype, accumulated the highest amount of unknown disaccharide 5, galactonic and phosphoric acids. The two most drought sensitive cultivars, Srpanjka and Ellvis, demonstrated different metabolic adjustment in response to the stress treatment. Srpanjka responded to drought by increasing the amount of glucose and fructose originated from hydrolyses of sucrose and accumulating unidentified sugar alcohols 1 and 2. In Ellvis, drought caused inhibition of photosynthetic carbon metabolism, as evidence by the decreased Pn, gs, RWC and accumulation levels of sugar metabolites (sucrose, glucose and fructose). The results revealed the differences in metabolic response to drought among the genotypes, which drew attention on metabolites related with general response and on those metabolites which are part of specific response that may play an important role in drought tolerance.

Dataset Information

Genetic Diversity and Population Structure of F_3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

Publications

Genetic Diversity and Population Structure of F<sub>3:6</sub> Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

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Dataset Information

Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

Publications

Genetic Diversity and Population Structure of F<sub>3:6</sub> Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Genetic Diversity and Population Structure of F_3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.