Analysis of genetic diversity, population structure and linkage disequilibrium in elite cotton (Gossypium L.) germplasm in India

An understanding of the level of genetic diversity is a prerequisite for designing efficient breeding programs. Fifty-one cultivars of four cotton species (Gossypium hirsutum, G. barbadense, G. herbaceum and G. arboreum) representing core collections at four major cotton research stations with a wide range of eco-geographical regions in India were examined for the level of genetic diversity, distinct subpopulations and the level of linkage disequilibrium (LD) using 1100 amplified fragment length polymorphism (AFLP) markers with 16 primer pairs combinations. The AFLP markers enabled a reliable assessment of inter- and intra-specific genetic variability with a heterogeneous genetic structure. Higher genetic diversity was noticed in G. herbaceum, followed by G. arboreum. The genetic diversity in tetraploid cotton species was found to be less than that in the diploid species. The genotypes VAGAD, RAHS14, IPS187, 221 557, Jayhellar of G. herbaceum and 551, DLSA17, 221 566 of G. arboreum were identified as the most diverse parents, useful for quantitative trait loci (QTL) analysis in diploid cotton. Similarly, LRA 5166, AS3 and MCU5 of G. hirsutum and B1, B3, Suvin of G. barbadense were most diverse to develop mapping populations for fibre quality. The internal transcribed spacer sequences were sufficient to resolve different species and subspecies of diploid cotton. Low level of genome-wide LD was detected in the entire collection (r2 = 0.07) as well as within the four species (r2 = 0.11–0.15). A strong agreement was noticed between the clusters constructed on the basis of morphological and genotyping data.

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Morphological description of a novel synthetic allotetraploid(A1A1G3G3) of Gossypium herbaceum L.and G.nelsonii Fryx. suitable for disease-resistant breeding applications

PLoS ONE ◽

10.1371/journal.pone.0242620 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0242620

Author(s):

Xiaomin Yin ◽

Rulin Zhan ◽

Yingdui He ◽

Shun Song ◽

Lixia Wang ◽

...

Keyword(s):

Chromosome Doubling ◽

Diploid Species ◽

Morphological Description ◽

Tetraploid Cotton ◽

Distant Hybridization ◽

Cotton Species ◽

Cotton Plants ◽

Wild Cotton ◽

Diploid Cotton ◽

Gossypium Herbaceum

Wild species of Gossypium ssp. are an important source of traits for improving commercial cotton cultivars. Previous reports show that Gossypium herbaceum L. and Gossypium nelsonii Fryx. have better disease resistance characteristics than commercial cotton varieties. However, chromosome ploidy and biological isolation make it difficult to hybridize diploid species with the tetraploid Gossypium hirsutum L. We developed a new allotetraploid cotton genotype (A1A1G3G3) using a process of distant hybridization within wild cotton species to create new germplasms. First of all, G. herbaceum and G. nelsonii were used for interspecific hybridization to obtain F1 generation. Afterwards, apical meristems of the F1 diploid cotton plants were treated with colchicine to induce chromosome doubling. The new interspecific F1 hybrid and S1 cotton plants originated from chromosome duplication, were tested via morphological and molecular markers and confirmed their tetraploidy through flowrometric and cytological identification. The S1 tetraploid cotton plants was crossed with a TM-1 line and fertile hybrid offspring were obtained. These S2 offsprings were tested for resistance to Verticillium wilt and demonstrated adequate tolerance to this fungi. The results shows that the new S1 cotton line could be used as parental material for hybridization with G. hirsutum to produce pathogen-resistant cotton hybrids. This new S1 allotetraploid genotype will contributes to the enrichment of Gossypium germplasm resources and is expected to be valuable in polyploidy evolutionary studies.

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Genetic Diversity of the Two Commercial Tetraploid Cotton Species in theGossypiumDiversity Reference Set

Journal of Heredity ◽

10.1093/jhered/esw004 ◽

2016 ◽

Vol 107 (3) ◽

pp. 274-286 ◽

Cited By ~ 23

Author(s):

Lori L. Hinze ◽

Elodie Gazave ◽

Michael A. Gore ◽

David D. Fang ◽

Brian E. Scheffler ◽

...

Keyword(s):

Genetic Diversity ◽

Tetraploid Cotton ◽

Reference Set ◽

Cotton Species

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Wheat Genetic Resources in Nepal

Nepal Agriculture Research Journal ◽

10.3126/narj.v7i0.1859 ◽

1970 ◽

Vol 7 ◽

pp. 1-10

Author(s):

BK Joshi ◽

A Mudwari ◽

MR Bhatta

Keyword(s):

Genetic Diversity ◽

Gene Pool ◽

Diploid Species ◽

Genetic Erosion ◽

Wild Relatives ◽

Gene Pools ◽

Wheat Cultivars ◽

Cereal Breeding ◽

Wide Range ◽

Wheat Gene

Genetic diversity must be maintained and utilized for sustainable agriculture development. Theamount of genetic diversity in the country depends on the number and diversity of the originalancestors involved in the creation of a germplasm pool, wild relatives and existing landraces.The objective of this research was to study the diversity of wheat gene pool present in theNepalese bread wheat cultivars and landraces that could help for developing conservation andutilization strategy effectively. We examined the pedigrees of 35 Nepalese wheat cultivars andsurveyed the literature for distribution of landraces and wild relatives of wheat. Cultivatedlandraces of spring and winter type, wild landraces and diploid species of wheat are found inNepal. There are 35 improved wheat cultivars, 540 landraces and 10 wild relatives of wheat.Crosses between winter and spring wheat gene pools are far more common and offer a newsource of diversity. Mexico, India and Nepal are the origin countries for 35 cultivars. In Nepalfour cultivars were bred and developed using foreign landraces and maximum number ofcultivars was developed in Mexico. Lerma 52, first improved cereal variety to be released in thehistory of cereal breeding in Nepal was released in 1960. A total of 89 ancestors originated in 22different countries were used to develop these cultivars. Highest number of ancestors was fromIndia. Ancestors of both aestivum and durum species having winter, spring and intermediategrowth habit indicated the collection of wide gene pool. Most of the ancestors were aestivum(76.40%) and spring growth habit (57.31%). Modern varieties are replacing the landraces andimproved old varieties resulted in the genetic erosion. Therefore, in situ, on farm and ex situconservations are necessary for maintaining these genetic variations. Unutilization of locallandraces in breeding program may be the major factor that causes to accelerate the geneticerosion. Gene pool from these landraces along with international gene pool could make towardssuccess in developing high yielding cultivars with wide adaptability. In this study, cultivars andlandraces surveyed represent a wide range of variation for different areas of origin andadaptation.Key words: Ancestor; landrace; origin; wheat gene poolDOI: 10.3126/narj.v7i0.1859Nepal Agriculture Research Journal Vol.7 2006 pp.1-10

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Population Genetic Structure of Septoria passerinii in Northern Great Plains Barley

Phytopathology ◽

10.1094/phyto-97-8-0938 ◽

2007 ◽

Vol 97 (8) ◽

pp. 938-944 ◽

Cited By ~ 6

Author(s):

S. H. Lee ◽

S. M. Neate

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

North Dakota ◽

Population Genetic Structure ◽

Population Differentiation ◽

Population Genetic ◽

Genotypic Diversity ◽

Aflp Markers ◽

Northern Great Plains ◽

Geographical Regions

The genetic structure of Septoria passerinii from nine field populations was examined at several scales (within lesions, among lesions in a leaf, among leaves in a field, and among fields in North Dakota and western Minnesota) by using amplified fragment length polymorphism (AFLP) markers. A total of 390 isolates were sampled from seven barley fields located in North Dakota and two barley fields located nearby in western Minnesota in 2003 and 2004. Based on 57 polymorphic AFLP markers, AFLP DNA fingerprints identified 176 different genotypes among 390 (non-clone-corrected) isolates in nine different fields. In two intensively sampled sites, ND16 (Williston, ND) and ND17 (Langdon, ND), only one to four different genotypes were found within a lesion. A higher level of genetic and genotypic diversity was found within a leaf in which six to nine different genotypes were found from lesions on a leaf. The genetic diversity within a leaf was similar to the genetic diversity within a field. The average genetic diversity (H) within a field across all AFLP loci was approximately 0.3, except at site ND12 (Carrington, ND) where it was 0.16. Genotypic diversity was high in all populations, and with the exception of ND15 (Rothsay, MN), very low multilocus linkage disequilibrium values ( rd) were found in all populations. The population differentiation, GST, was relatively high (GST = 0.238) among the nine populations due to the high GST in ND12, ND14 (Twin Valley, MN), and ND15. Population differentiation without those three populations was 0.09. A lack of correlation between geographical distance and genetic distance was found, suggesting the potential for a high level of gene flow between different geographical regions. The population genetic structure described in this study for S. passerinii in North Dakota and western Minnesota is consistent with that of a sexually reproducing fungus.

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Comparative Functional Studies on Two Diploid Cotton Genomes Reveals Functional Differences of Basic Helix-loop-helix Proteins in Arabidopsis Trichome Initiation

Annual Research & Review in Biology ◽

10.9734/arrb/2019/v34i230146 ◽

2020 ◽

pp. 1-12

Author(s):

Anh Phu Nam Bui ◽

Vimal Kumar Balasubramanian ◽

Thuan-Anh Nguyen-Huu ◽

Tuan-Loc Le ◽

Hoang Dung Tran

Keyword(s):

Diploid Species ◽

Natural Phenomenon ◽

Tetraploid Cotton ◽

D Genome ◽

Genome Species ◽

Functional Studies ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Cotton Species ◽

A Genome

Background: The cultivated tetraploid cotton species (AD genomes) was originated from two ancestral diploid species (A and D genomes). While the ancestral A-genome species produce spinnable fibers, the D- genome species do not. Cotton fibers are unicellular trichomes originating from seed coat epidermal cells, and currently there is an immense interest in understanding the process of fiber initiation and development. Current knowledge demonstrates that there is a great of deal of resemblance in initiation mechanism between by Arabidopsis trichome and cotton fiber. Methodology: In this study, we performed comparative functional studies between A genome and D-genome species in cotton by using Arabidopsis trichome initiation as a model. Four cotton genes TTG3, MYB2, DEL61 and DEL65 were amplified from A-genome and D-genome species, and transformed into their homolog trichomeless mutants Arabidopsis ttg1, gl1, and gl3egl3, respectively. Results: Our data indicated that the transgenic plants expressing TTG3 and MYB2 genes from A-genome and D-genome species complement the ttg1 and gl1 mutants, respectively. We also discovered complete absences of two functional basic helix loop helix (bHLH) proteins (DEL65/DEL61) in D- diploid species and one (DEL65) that is functional in A-genome species, but not from D-genome species. This observation is consistent with the natural phenomenon of spinnable fiber production in A- genome species and absence in D-genome species.

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DArT-seq based SNP analysis of diversity, population structure and linkage disequilibrium among 274 cowpea (Vigna unguiculata L. Walp.) accessions

10.21203/rs.3.rs-50796/v2 ◽

2020 ◽

Author(s):

Frejus Ariel Kpedetin Sodedji ◽

Symphorien Agbahoungba ◽

Eric Echikintho Agoyi ◽

Konoutan Médard Kafoutchoni ◽

Ho-Youn Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Vigna Unguiculata ◽

Central Africa ◽

Inbred Lines ◽

Snp Analysis ◽

Genome Wide Association Studies ◽

Population Structure Analysis ◽

Geographical Regions

Abstract Background: Genetic diversity in a germplasm is crucial for continuous improvement of crop varieties. A panel of 274 cowpea ( Vigna unguiculata L.) accessions of unknown genetic diversity was assembled from diverse sources. This study used 3127 SNP markers, generated with the diversity array technology (DArT), to assess genetic diversity, population structure and linkage disequilibrium (LD) in the assembled germplasm. Results: The population structure analysis inferred three subpopulations within the germplasm, which was confirmed by Neighbour-Joining (NJ) clustering and principal component analysis (PCA). Low genetic distances (0.005 to 0.44) were observed between accessions. Accessions from Africa; West and Central Africa (113 accessions), East and Central Africa (93 accessions), and Asia (53 accessions) were predominant in the germplasm; and distributed across all subpopulations. High fixation indexes (0.48≤F ST ≤0.56) were obtained for the inferred subpopulations. AMOVA revealed a very large contribution of within subpopulations variation to the observed genetic variation in the germplasm. However, the expected heterozygosity (He) was higher than the observed heterozygosity (Ho), indicating high proportion of inbred lines in the germplasm. Linkage Disequilibrium (LD) was observed in the germplasm, which showed a low decay at longer physical distance between markers in the genome. Conclusions: Significant genetic structuration exists in the assembled cowpea germplasm which shows that there is a potential for improvement of the crop. The subgroups consisted mainly of inbred lines which, although from different geographical regions shared alleles in common reflecting high movement of seeds and exchange of germplasm between regions. The presence of linkage disequilibrium in the germplasm paves a way for prospective whole genome-wide association studies in cowpea for quality attributes and important agronomic traits.

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Molecular cloning and expression of a cDNA encoding a microsomal w-6 fatty acid desaturase from cotton (Gossypium hirsutum)

Functional Plant Biology ◽

10.1071/pp98118 ◽

1999 ◽

Vol 26 (2) ◽

pp. 101 ◽

Cited By ~ 33

Author(s):

Qing Liu ◽

Surinder P. Singh ◽

Curt L. Brubaker ◽

Peter J. Sharp ◽

Allan G. Green ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Blot Analysis ◽

Northern Blot Analysis ◽

Fatty Acid Desaturase ◽

Cloning And Expression ◽

Tetraploid Cotton ◽

Coding Region ◽

Gossypium Hirsutum L ◽

Cotton Species ◽

Diploid Cotton

A cDNA (ghFAD2-1) encoding a seed-specific microsomal ω-6 desaturase was isolated from a cotton (Gossypium hirsutum L. cv. Deltapine-16) embryo cDNA library. The deduced amino acid sequence showed substantial similarity to other plant microsomal ω-6 desaturases. Northern blot analysis indicated that the ghFAD2-1 transcript was specifically induced during embryo development and expression of the transcript could not be detected in leaves. Southern blot analysis using the coding region and 3′ untranslated region of ghFAD2-1 revealed that microsomal ω-6 desaturase in cotton is encoded by a small multigene family. There are at least two copies of ghFAD2-1 in two tetraploid cotton species (G. hirsutum L. and G. barbadense L.) and at least one copy in diploid cotton species (G. herbaceum L., G. raimondii Ulbrich and G. robinsonii Mueller).

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Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. var durum) collection

PLoS ONE ◽

10.1371/journal.pone.0218562 ◽

2019 ◽

Vol 14 (6) ◽

pp. e0218562 ◽

Cited By ~ 5

Author(s):

Pablo Federico Roncallo ◽

Valeria Beaufort ◽

Adelina Olga Larsen ◽

Susanne Dreisigacker ◽

Viviana Echenique

Keyword(s):

Genetic Diversity ◽

Linkage Disequilibrium ◽

Durum Wheat ◽

Triticum Turgidum ◽

Aflp Markers

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DArT-seq based SNP analysis of diversity, population structure and linkage disequilibrium among 274 cowpea (Vigna unguiculata L. Walp.) accessions

10.21203/rs.3.rs-50796/v1 ◽

2020 ◽

Author(s):

Frejus Ariel Kpedetin Sodedji ◽

Symphorien Agbahoungba ◽

Eric Echikintho Agoyi ◽

Konoutan Médard Kafoutchoni ◽

Ho-Youn Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Vigna Unguiculata ◽

Central Africa ◽

Inbred Lines ◽

Large Contribution ◽

Snp Analysis ◽

Genome Wide Association Studies ◽

Geographical Regions

Abstract Background: Genetic diversity in a germplasm is crucial for continuous improvement of crop varieties. A panel of 274 cowpea (Vigna unguiculata L.) accessions of unknown genetic diversity was assembled from diverse sources. This study used 3127 SNP markers, generated with the diversity array technology (DArT), to assess genetic diversity, population structure and linkage disequilibrium (LD) in the assembled germplasm.Results: The structure analysis inferred three subpopulations within the germplasm, which was confirmed by Neighbour-Joining (NJ) clustering and principal component analysis (PCA). Low genetic distances (0.005 to 0.44) were observed between accessions. Accessions from Africa; West and Central Africa (113 accessions), East and Central Africa (93 accessions), and Asia (53 accessions) were predominant in the germplasm; and distributed across all subpopulations. High fixation indexes (0.48 ≤ FST≤0.56) were obtained for the inferred subpopulations. AMOVA revealed a very large contribution (99%) of within subpopulations variation to the observed genetic variation in the germplasm. However, the expected heterozygosity (He) was higher than the observed heterozygosity (Ho), indicating high proportion of inbred lines in the germplasm. Linkage Disequilibrium (LD) was observed in the germplasm, particularly on chromosome 6, which showed a low decay along the physical genetic distance between markers in the genome.Conclusions: Significant genetic structuration exists in the assembled cowpea germplasm which shows there is a potential for improvement of the crop. The subgroups consisted mainly of inbred lines which, although from different geographical regions shared alleles in common reflecting high movement of seeds and exchange of germplasm between regions. The presence of linkage disequilibrium in the germplasm paves a way for prospective whole genome-wide association studies in cowpea for quality attributes and important agronomic traits.

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Models of archaic admixture and recent history from two-locus statistics

10.1101/489401 ◽

2018 ◽

Cited By ~ 4

Author(s):

Aaron P. Ragsdale ◽

Simon Gravel

Keyword(s):

Genetic Diversity ◽

Linkage Disequilibrium ◽

Evolutionary Biology ◽

Demographic History ◽

Population History ◽

Human Populations ◽

Evolutionary Models ◽

Human History ◽

Wide Range ◽

Archaic Admixture

AbstractWe learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4-8% genetic ancestry to individuals in world-wide populations.Author SummaryThroughout human history, populations have expanded and contracted, split and merged, and ex-changed migrants. Because these events affected genetic diversity, we can learn about human history by comparing predictions from evolutionary models to genetic data. Here, we show how to rapidly compute such predictions for a wide range of diversity measures within and across populations under complex demographic scenarios. While widely used models of human history accurately predict common measures of diversity, we show that they strongly underestimate the co-occurence of low frequency mutations within human populations in Asia, Europe, and Africa. Models allowing for archaic admixture, the relatively recent mixing of human populations with deeply diverged human lineages, resolve this discrepancy. We use such models to infer demographic models that include both recent and ancient features of human history. We recover the well-characterized admixture of Neanderthals in Eurasian populations, as well as admixture from an as-yet unknown diverged human population within Africa, further suggesting that admixture with deeply diverged lineages occurred multiple times in human history. By simultaneously testing model predictions for a broad range of diversity statistics, we can assess the robustness of common evolutionary models, identify missing historical events, and build more informed models of human demography.

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