Diversity of white Guinea yam (Dioscorea rotundata Poir.) cultivars from Benin as revealed by agro-morphological traits and SNP markers

Abstract White Guinea yam (Dioscorea rotundata Poir.) is indigenous to West Africa, a region that harbours the crop's tremendous landrace diversity. The knowledge and understanding of local cultivars’ genetic diversity are essential for properly managing genetic resources, conservation, sustainable use and their improvement through breeding. This study aimed to dissect phenotypic and molecular diversity of white yam cultivars from Benin using agro-morphological and single nucleotide polymorphism (SNP) markers. Eighty-eight Beninese white Guinea yam cultivars collected through a countrywide ethnobotanical survey were phenotyped with 53 traits and genotyped with 9725 DArT-SNP. Multivariate analysis using phenotypic traits revealed 30 traits as most discriminative and explained up to 80.78% of cultivars’ phenotypic variation. Assessment of diversity indices such as Shannon–Wiener (H′), inverse Shannon (H.B.), Simpson's (λ) index and Pilou evenness (J) based molecular and phenotypic data depicted a moderate genetic diversity in Beninese white Guinea yam cultivars. Genetic differentiation of cultivars among country production zones was low due to the high exchange of planting materials among farmers of different regions. However, there was high genetic diversity within regions. Hierarchical clusters (HCs) on phenotypic data revealed the presence of two groups while HCs based on the SNP markers and the combined analysis identified three genetic groups. Our result provided valuable insights into the Beninese white Guinea yam diversity for its proper conservation and improvement through breeding.

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Evaluation of genetic variability among “Early Mature”Juglans regiausing microsatellite markers and morphological traits

PeerJ ◽

10.7717/peerj.3834 ◽

2017 ◽

Vol 5 ◽

pp. e3834 ◽

Cited By ~ 3

Author(s):

Aziz Ebrahimi ◽

Abdolkarim Zarei ◽

Mojtaba Zamani Fardadonbeh ◽

Shaneka Lawson

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Normal Growth ◽

Diversity Indices ◽

Shannon Index ◽

Phenotypic Trait ◽

Phenotypic Traits ◽

High Genetic Diversity ◽

Early Maturation ◽

Persian Walnut

Limiting the juvenile phase and reducing tree size are the two main challenges for breeders to improve most fruit crops. Early maturation and dwarf cultivars have been reported for many fruit species. “Early mature” and low vigor walnut genotypes were found among seedlings of Persian walnut. Nine microsatellite markers were used to evaluate genetic diversity among “Early Mature” Persian walnut accessions and provide a comparison with “normal growth” accessions. Six maturation related characteristics were also measured in “Early Mature” samples. Phenotypic traits and diversity indices showed relatively high levels of genetic diversity in “Early Mature” seedlings and indicated high differentiation between individuals. Seedling height, the most diverse phenotypic trait, has an important role in the clustering of “Early Mature” accessions. The “Early Mature” type had higher number of alleles, number of effective allele, and Shannon index compared to the “Normal Growth” group. The two types of studied walnuts had different alleles, with more than half of produced alleles specific to a specific group. “Early Mature” and “Normal Growth” walnuts had 27 and 17 private alleles, respectively. Grouping with different methods separated “Early Mature” and “Normal Growth” samples entirely. The presence of moderate to high genetic diversity in “Early Mature” walnuts and high genetic differentiation with “Normal Growth” walnuts, indicated that “Early Mature” walnuts were more diverse and distinct from “Normal Growth” samples. Moreover, our results showed SSR markers were useful for differentiating between “Early Mature” and “Normal Growth” walnuts. A number of identified loci have potential in breeding programs for identification of “Early Mature” walnuts at the germination phase.

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Paternity Assignment in White Guinea Yam (Dioscorea Rotundata) Half-Sib Progenies from Polycross Mating Design Using SNP Markers

Plants ◽

10.3390/plants9040527 ◽

2020 ◽

Vol 9 (4) ◽

pp. 527 ◽

Cited By ~ 2

Author(s):

Prince E. Norman ◽

Agre A. Paterne ◽

Agyemang Danquah ◽

Pangirayi B. Tongoona ◽

Eric Y. Danquah ◽

...

Keyword(s):

Cost Effective ◽

Snp Markers ◽

Open Pollination ◽

Dioscorea Rotundata ◽

Mating Design ◽

Foreign Pollen ◽

Paternal Identity ◽

Or Gene ◽

Guinea Yam

White Guinea yam is mostly a dioecious outcrossing crop with male and female flowers produced on distinct plants. Fertile parents produce high fruit set in an open pollination polycross block, which is a cost-effective and convenient way of generating variability in yam breeding. However, the pollen parent of progeny from polycross mating is usually unknown. This study aimed to determine paternity in white Guinea yam half-sib progenies from polycross mating design. A total of 394 half-sib progenies from random open pollination involving nine female and three male parents was genotyped with 6602 SNP markers from DArTSeq platform to recover full pedigree. A higher proportion of expected heterozygosity, allelic richness, and evenness were observed in the half-sib progenies. A complete pedigree was established for all progenies from two families (TDr1685 and TDr1688) with 100% accuracy, while in the remaining families, paternity was assigned successfully only for 56 to 98% of the progenies. Our results indicated unequal paternal contribution under natural open pollination in yam, suggesting unequal pollen migrations or gene flow among the crossing parents. A total of 3.8% of progenies lacking paternal identity due to foreign pollen contamination outside the polycross block was observed. This study established the efficient determination of parental reconstruction and allelic contributions in the white Guinea yam half-sib progenies generated from open pollination polycross using SNP markers. Findings are useful for parental reconstruction, accurate dissection of the genetic effects, and selection in white Guinea yam breeding program utilizing polycross mating design.

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Assessing genetic variation for heat stress tolerance in Indian bread wheat genotypes using morpho-physiological traits and molecular markers

Plant Genetic Resources ◽

10.1017/s1479262116000241 ◽

2016 ◽

Vol 15 (6) ◽

pp. 539-547 ◽

Cited By ~ 5

Author(s):

P. Sharma ◽

S. Sareen ◽

M. Saini ◽

Shefali

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Heat Stress ◽

Molecular Markers ◽

Heat Tolerance ◽

Polymorphic Information Content ◽

Physiological Traits ◽

Phenotypic Traits ◽

Phenotypic Data ◽

Wheat Genotypes

AbstractHeat stress greatly limits the productivity of wheat in many regions. Knowledge on the degree of genetic diversity of wheat varieties along with their selective traits will facilitate the development of high yielding, stress-tolerant wheat cultivar. The objective of this study were to determine genetic variation in morpho-physiological traits associated with heat tolerance in 30 diverse wheat genotypes and to examine genetic diversity and relationship among the genotypes varying heat tolerance using molecular markers. Phenotypic data of 15 traits were evaluated for heat tolerance under non-stress and stress conditions for two consecutive years. A positive and significant correlation among cell membrane stability, canopy temperature depression, biomass, susceptibility index and grain yield was shown. Genetic diversity assessed by 41 polymorphic simple sequence repeat (SSR) markers was compared with diversity evaluated for 15 phenotypic traits averaged over stress and non-stress field conditions. The mean polymorphic information content for SSR value was 0.38 with range of 0.12–0.75. Based on morpho-physiological traits and genotypic data, three groups were obtained based on their tolerance (HHT, MHT and LHT) levels. Analysis of molecular variance explained 91.7% of the total variation could be due to variance within the heat tolerance genotypes. Genetic diversity among HHT was higher than LHT genotypes and HHT genotypes were distributed among all cluster implied that genetic basis of heat tolerance in these genotypes was different thereby enabling the wheat breeders to combine these diverse sources of genetic variation to improve heat tolerance in wheat breeding programme.

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Genetic diversity of long-established populations of Elaeis guineensis jacquin (Arecaceae)

Revista Brasileira de Fruticultura ◽

10.1590/0100-29452019023 ◽

2019 ◽

Vol 41 (4) ◽

Author(s):

Kyvia Pontes Teixeira das Chagas ◽

Ageu da Silva Monteiro Freire ◽

Luciana Gomes Pinheiro ◽

Cristiane Gouvêa Fajardo ◽

Fábio de Almeida Vieira

Keyword(s):

Genetic Diversity ◽

Elaeis Guineensis ◽

Sustainable Use ◽

Diversity Indices ◽

Ex Situ ◽

Effective Population ◽

Infinite Allele Model ◽

Population Decrease ◽

Stepwise Mutation ◽

Conservation Projects

Abstract This study aimed to estimate the genetic diversity of three Elaeis guineensis populations in Rio Grande do Norte state, as well as to verify the decreases in effective population size. The population with the highest polymorphism was MAT (Mata) with+ 57 loci (72%), followed by RIA (Riacho) with 54 loci (68%) and HOR (Horta) with 34 loci (43.03%). The RIA population was shown to be the most genetically diverse, with Nei (h = 0.28) and Shannon (I = 0.41) diversity indices. There was high genetic differentiation among populations (AMOVA, analysis of molecular variance = 42%), which was separated into three distinct genetic groups according to a Bayesian analysis. There was a significant population decrease (P < 0.05) for the HOR population in the IAM (infinite allele model) and SMM (stepwise mutation model), and for the RIA population in the IAM. The data obtained in this study may support ex-situ conservation projects for Elaeis guineensis, contributing to the selection of genotypes and their sustainable use.

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ISSR analysis of two founding plant species on the volcanic island Surtsey, Iceland: grass versus shrub

Surtsey research ◽

10.33112/surtsey.13.2 ◽

2015 ◽

Vol 13 ◽

pp. 17-30 ◽

Cited By ~ 2

Author(s):

Agnieszka Sutkowska ◽

Kesara Anamthawat-Jónsson ◽

Borgthór Magnússon ◽

Wojciech Bąba ◽

Józef R. Mitka

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Spatial Genetic Structure ◽

Diversity Indices ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Plant Colonization ◽

Common Source ◽

High Genetic Diversity ◽

Early Arrival

Prior to the present study there was limited knowledge about the genetic basis of plant colonization on the 50-year-old island of Surtsey, South Iceland. The aim here was to compare genetic structure of two contrasting species, Festuca rubra (arctic fescue) and Empetrum nigrum (crowberry), which have colonized Surtsey since 1973 and 1993, respectively. Inter-simple sequence repeat (ISSR) markers were used to assess genetic diversity and population structure. Two census periods were compared: 1996-1997 and 2005-2006. Using six ISSR primers, we obtained 103 and 139 discernible DNA fragments from F. rubra and E. nigrum respectively. Although the two species displayed similarly high genetic diversity indices (h = 0.238 and 0.235; I = 0.384 and 0.380, respectively), they differed significantly in their genetic profiles. Festuca was genetically structured at the subpopulation level (FST = 0.034, p = 0.007), whereas Empetrum showed a lack of genetic differentiation. A Bayesian STRUCTURE computation further revealed temporal and spatial genetic structure of the species. The early arrival grass F. rubra has expanded from a local genepool. The population was however initially established from different sources, forming a genetic melting pot on Surtsey. On the other hand, the late arrival shrub E. nigrum probably derived from a common source of immigrants.

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Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

Genes ◽

10.3390/genes10090676 ◽

2019 ◽

Vol 10 (9) ◽

pp. 676 ◽

Cited By ~ 3

Author(s):

Farahani ◽

Maleki ◽

Mehrabi ◽

Kanouni ◽

Scheben ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Large Scale ◽

Principal Component ◽

Snp Markers ◽

Genome Diversity ◽

High Genetic Diversity ◽

Breeding Programs ◽

Population Structure Analysis

Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.

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Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

BMC Genetics ◽

10.1186/s12863-020-00914-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Nelia Nkhoma ◽

Hussein Shimelis ◽

Mark D. Laing ◽

Admire Shayanowako ◽

Isack Mathew

Keyword(s):

Genetic Diversity ◽

Grain Yield ◽

Vigna Unguiculata ◽

Polymorphic Information Content ◽

Snp Markers ◽

Phenotypic Traits ◽

Environment Interaction ◽

Lattice Design ◽

Cultivar Development ◽

Parental Lines

Abstract Background Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to determine the extent of genetic diversity present among a collection of cowpea accessions from Zambia and Malawi using phenotypic traits and single nucleotide polymorphism (SNP) markers and, to select distinct and complementary parental lines for cultivar development. One hundred cowpea genotypes were evaluated for agronomic traits in two selected sites in Zambia, using a 10 × 10 alpha lattice design with two replications. Ninety-four of the test genotypes were profiled with 14,116 SNP markers. Results Number of pods plant− 1 (NPP), pod length (PDL), and number of seeds pod− 1 (NSP), were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes such as CP411, CP421, CP645, CP732, Chimponongo, and MS1–8–1-4 exhibited higher grain yield of > 1200 kg/ha with excellent performance in yield components such as NSP, PDL, HSW and GYD. Grain yield had significant (p < 0.05) associations with NPP (r = 0.50), NSP (r = 0.46) and PDL (r = 0.42) useful for simultaneous selection for yield improvement in cowpea. The SNP markers revealed gene diversity and polymorphic information content of 0.22 and 0.17, respectively, showing that the tested cowpea accessions were genetically diverse. Test genotypes were classified into four genetic groups irrespective of source of collection allowing selection and subsequent crosses to develop breeding populations for cultivar development. Conclusions Genotypes Bubebe, CP411, CP421, CP645, Chimponogo and MS1–8–1-4 were identified to be the most genetically divergent and high yielding making them ideal parental lines for breeding. This study provided a baseline information and identified promising cowpea genetic resources for effective breeding and systematic conservation.

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Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

10.21203/rs.3.rs-26693/v2 ◽

2020 ◽

Author(s):

Nelia Nkhoma ◽

Hussein Shimelis ◽

Mark Laing ◽

Admire Shayanowako ◽

Isack Mathew

Keyword(s):

Genetic Diversity ◽

Grain Yield ◽

Vigna Unguiculata ◽

Polymorphic Information Content ◽

Snp Markers ◽

Phenotypic Traits ◽

Environment Interaction ◽

Lattice Design ◽

Cultivar Development ◽

Parental Lines

Abstract Background: Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to determine the extent of genetic diversity present among a collection of cowpea accessions from Zambia and Malawi using phenotypic traits and single nucleotide polymorphism (SNP) markers and, to select distinct and complementary parental lines for cultivar development. One hundred cowpea genotypes were evaluated for agronomic traits in two selected sites in Zambia, using a 10×10 alpha lattice design with two replications. Ninety-four of the test genotypes were profiled with 14,116 SNP markers. Results: Number of pods plant-1 (NPP), pod length (PDL), and number of seeds pod-1 (NSP), were significantly (p<0.05) affected by genotype × environment interaction effects. Genotypes such as CP411, CP421, CP645, CP732, Chimponongo, and MS1-8-1-4 exhibited higher grain yield of > 1200 kg/ha with excellent performance in yield components such as NSP, PDL, HSW and GYD. Grain yield had significant (p<0.05) associations with NPP (r=0.50), NSP (r=0.46) and PDL (r=0.42) useful for simultaneous selection for yield improvement in cowpea. The SNP markers revealed gene diversity and polymorphic information content of 0.22 and 0.17, respectively, showing that the tested cowpea accessions were genetically diverse. Test genotypes were classified into four genetic groups irrespective of source of collection allowing selection and subsequent crosses to develop breeding populations for cultivar development. Conclusions: Genotypes Bubebe, CP411, CP421, CP645, Chimponogo and MS1-8-1-4 were identified to be the most genetically divergent and high yielding making them ideal parental lines for breeding. This study provided a baseline information and identified promising cowpea genetic resources for effective breeding and systematic conservation.

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Whole Genome Diversity, Population Structure and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

10.20944/preprints201904.0321.v1 ◽

2019 ◽

Author(s):

Somayeh Farahani ◽

Mojdeh Maleki ◽

Rahim Mehrabi ◽

Homayoun Kanouni ◽

Reza Talebi

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Large Scale ◽

Principal Component ◽

Snp Markers ◽

Genome Diversity ◽

High Genetic Diversity ◽

Breeding Programs ◽

Population Structure Analysis

Characterization of genetic diversity, population structure and linkage disequilibrium is prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes were genotyped using DArTseq-Based SNP markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that covered by SNPs varied from 16236.36 kbp (LG8) to 67923.99 kbp (LG5), while LG4 showed higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6 and LG8 showed higher mean PIC value than average. Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and Discriminant Analysis of Principal Component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2≥0.8, while 2961 pairs of markers showed complete LD (r2=1) and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggesting the presence of a high genetic diversity among studied chickpea genotypes. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits such as seed yield, abiotic and biotic stresses and therefore can be efficiently used in breeding programs to improve chickpea.

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Genetic Diversity and Population Structure for Resistance and Susceptibility to Mastitis in Braunvieh Cattle

Veterinary Sciences ◽

10.3390/vetsci8120329 ◽

2021 ◽

Vol 8 (12) ◽

pp. 329

Author(s):

Mitzilin Zuleica Trujano-Chavez ◽

Reyna Sánchez-Ramos ◽

Paulino Pérez-Rodríguez ◽

Agustín Ruíz-Flores

Keyword(s):

Genetic Diversity ◽

Candidate Genes ◽

Genetic Resistance ◽

Principal Component ◽

Clinical Mastitis ◽

Snp Markers ◽

Economic Losses ◽

High Genetic Diversity ◽

A Value ◽

Candidate Loci

Mastitis is a disease that causes significant economic losses, since resistance to mastitis is a difficult trait to be improved due to its multifactorial occurrence. Therefore, our objective was to characterize a Mexican Braunvieh cattle population for genetic resistance and susceptibility to mastitis. We used 66 SNP markers for 45 candidate genes in 150 animals. The average heterozygosity was 0.445 ± 0.076, a value higher than those reported for some European breeds. The inbreeding coefficient was slightly negative for resistance to subclinical (−0.058 ± 0.055) and clinical (−0.034 ± 0.076) mastitis, possibly due to low selection for the immunological candidate genes that influence these traits. The genotypic profiles for the candidate loci per K-means group were obtained, as well as the group distribution through the graphics of the principal component analysis. The genotypic profiles showed high genetic diversity among groups. Resistance to clinical mastitis had the lowest presence of the heterozygous genotypes. Although the percentage of highly inbred animals (>50%) is up to 13.3%, there are highly heterozygous groups in terms of the studied traits, a favorable indicator of the presence of genetic diversity. The results of this study constitute evidence of the genetic potential of the Mexican Braunvieh population to improve mastitis-related traits.

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