Networking and Bayesian analyses of genetic affinity in cotton germplasm

Noormohammadi, Zahra; Sheidai, Masoud; Foroutan, Momeneh; Alishah, Omran

doi:10.1007/s13237-014-0123-y

Cited by 6 publications

(5 citation statements)

References 29 publications

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“…The results are quite congruent to prior taxonomic studies [2,3,66]. The average genetic distance (GD = 0.325) revealed the overall level of genetic diversity to be high among semi-wild and cultivated accessions; this finding is similar to earlier reports [26,67,68]. However, this estimate may be inflated since data from monomorphic SSR loci were excluded in the current study.…”

Section: Discussionsupporting

confidence: 92%

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Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

Ditta

Zhou

Cai

et al. 2018

IJMS

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This study evaluated the genetic diversity and population structures in a novel cotton germplasm collection comprising 132 diploids, including Glossypium klotzschianum and allotetraploid cotton accessions, including Glossypium barbadense, Glossypium darwinii, Glossypium tomentosum, Glossypium ekmanianum, and Glossypium stephensii, from Santa Cruz, Isabella, San Cristobal, Hawaiian, Dominican Republic, and Wake Atoll islands. A total of 111 expressed sequence tag (EST) and genomic simple sequence repeat (gSSR) markers produced 382 polymorphic loci with an average of 3.44 polymorphic alleles per SSR marker. Polymorphism information content values counted 0.08 to 0.82 with an average of 0.56. Analysis of a genetic distance matrix revealed values of 0.003 to 0.53 with an average of 0.33 in the wild cotton collection. Phylogenetic analysis supported the subgroups identified by STRUCTURE and corresponds well with the results of principal coordinate analysis with a cumulative variation of 45.65%. A total of 123 unique alleles were observed among all accessions and 31 identified only in G. ekmanianum. Analysis of molecular variance revealed highly significant variation between the six groups identified by structure analysis with 49% of the total variation and 51% of the variation was due to diversity within the groups. The highest genetic differentiation among tetraploid populations was observed between accessions from the Hawaiian and Santa Cruz regions with a pairwise FST of 0.752 (p < 0.001). DUF819 containing an uncharacterized gene named yjcL linked to genomic markers has been found to be highly related to tryptophan-aspartic acid (W-D) repeats in a superfamily of genes. The RNA sequence expression data of the yjcL-linked gene Gh_A09G2500 was found to be upregulated under drought and salt stress conditions. The existence of genetic diversity, characterization of genes and variation in novel germplasm collection will be a landmark addition to the genetic study of cotton germplasm.

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Section: Discussionsupporting

confidence: 92%

“…PCoA plots separated tetraploid cottons from diploid plants, supporting the AMOVA results. All these results are in good agreement with Noormohammadi et al’s genetic diversity analysis [ 68 ] between diploid and tetraploid accessions.…”

Section: Discussionsupporting

confidence: 91%

Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

Ditta

Zhou

Cai

et al. 2018

IJMS

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“…Neophytou et al (2022) following STRUCTURE analysis used the solutions for K = 2, 4 and 6 for further investigation considering the selection of the Douglas Fir trees for breeding purposes. Noormohammadi et al (2015) through STRUCTURE analysis identified 9 distinct population groups, while K-Means clustering suggested 2-3 major genetic subgroups in the present germplasm. They intend to use the obtained results to establish a better hybridization and selection plan for cotton.…”

Section: Resultsmentioning

confidence: 82%

Using of relatedness and heritability in a Eucalyptus benthamii trial for conservation and breeding

Souza,

Abreu,

Pappas

et al. 2023

Crop Breed. Appl. Biotechnol.

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We evaluated the genetic diversity, coancestry and heritability of an E. benthamii trial. The 115 individuals were genotyped (13 SSR) and had their height and diameter at breast height (dbh) measured. Heritability was estimated using the RR-BLUP and the pairwise kinship coefficient method. An average of nine alleles per locus was observed. The expected heterozygosity (0.655) was similar to the observed heterozygosity, with the estimated inbreeding (0.02) being low. The group coancestry (0.051) demonstrates that the trees are related to some degree. The trees were clustered in five groups using the Evanno's method. The average kinship within each group ranges from 0.042 to 0.082. The heritability estimated by RR-BLUP was low. The heritability estimated using the kinship coefficients is moderate, reaching estimated genetic gains of 14% for dbh. After knowing how genetic groups are distributed within the population, strategies for collecting, conserving, and using these germplasm resources can be performed.

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“…Use of efficient, low-cost and fast genetic screening method is a must for breeders to identify diverse parental genotypes when dealing with large cotton germplasm (VAN ESBROECK et al, 1998;SHEIDAI et al, 2007;SHEIDAI et al, 2008;TYAGI et al, 2014;NOORMOHAMMADI et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

“…Different types of molecular markers were used to study genetic diversity in cotton. These molecular markers were: Random amplified polymorphic DNA (RAPD), allozymes, restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSRs), and inter-simple sequence repeats (ISSRs) as well as retrotrasposon based molecular marker (REMAP) (see for example, VAN ESBROECK et al, 1998;ABDALLA et al, 2001;SHEIDAI et al, 2007;SHEIDAI et al, 2008;KANTARTZI et al, 2009;NOORMOHAMMADI et al, 2015;NOORMOHAMMADI et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Genetic finger printing of cotton cultivars by ISSR molecular markers

2018

Self Cite

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Gossypium hirsutum is one of the main tetraploid cotton species that is cultivated throughout the world. Due to continuous selection of cotton cultivars for specific agronomic traits, the genetic variability within the cultivars decrease that lead to genetic erosion. To tackle the problem of reduced genetic variability, we should track all available genetic diversity within cotton germplasm and use them for inter-specific and intra-specific hybridization and produce new elite cotton cultivars. Therefore, the present study used ISSR molecular markers to illustrate genetic variability in 13 tetraploid cotton genotypes (Gossypium hirsutum L.) and to categorize these genotypes based on genetic affinity. 65 cotton plants were studied. The results identified private bands in the studied genotypes, while Network and STRUCTURE analyses of molecular data obtained grouped the genotypes with genetic affinity together. Some of the genotypes differed in their genetic content from the others; therefore, studying the genetic and agronomic variability within available cultivars is very important and produced data to broaden the gene pool for planning further hybridization in cotton.

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Networking and Bayesian analyses of genetic affinity in cotton germplasm

Cited by 6 publications

References 29 publications

Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

Using of relatedness and heritability in a Eucalyptus benthamii trial for conservation and breeding

Genetic finger printing of cotton cultivars by ISSR molecular markers

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