Exploring genetic diversity and quality traits in a collection of onion (Allium cepa L) landraces from north-west Spain

Seventeen onion landraces from North-West Spain were evaluated using microsatellites markers. Eleven polymorphic markers identified 32 alleles in the whole collection, with an average of 2.9 alleles per locus. High values of observed (mean of 0.45) and expected heterozigosity (mean of 0.51) were detected for the majority of loci. Wright?s fixation index confirmed an excess of heterozygotes and a low level of inbreeding within the collection. Multivariate analyses revealed that Oimbra was the most distinctive genotype. The remaining 16 onion genotypes were in part assorted according to some morphological traits of bulbs. Pungency and solid soluble content highly varied among landraces and bulbs. Five landraces were classified as sweet, whereas 9 possessed medium pungency and 3 were recorded as pungent. This onion collection represents a useful source of genetic heterogeneity that might be exploited in breeding programs for the generation of new onion varieties that satisfy consumer demands.

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Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Scientific Reports ◽

10.1038/s41598-021-94802-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Grimar Abdiel Perez ◽

Pumipat Tongyoo ◽

Julapark Chunwongse ◽

Hans de Jong ◽

Anucha Wongpraneekul ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Collection ◽

Snp Markers ◽

Fixation Index ◽

Breeding Programs ◽

Total Fixation ◽

Unrooted Phylogenetic Tree ◽

Luffa Acutangula ◽

Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers

Brazilian Journal of Biology ◽

10.1590/1519-6984.226889 ◽

2020 ◽

Author(s):

R. H. Sammour ◽

M. A. Karam ◽

Y. S. Morsi ◽

R. M. Ali

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Brassica Rapa ◽

Phylogenetic Relationships ◽

Fixation Index ◽

Distribution Area ◽

Enzyme Analysis ◽

Breeding Programs ◽

Expected Heterozygosity ◽

Wide Range

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

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Genetic diversity and population structure of Algerian chickpea (Cicer arietinum) genotypes: use of agro-morphological traits and molecular markers linked or not linked to the gene or QTL of interest

Crop and Pasture Science ◽

10.1071/cp19255 ◽

2020 ◽

Vol 71 (2) ◽

pp. 155

Author(s):

Djihad Bellemou ◽

Teresa Millàn ◽

Juan Gil ◽

Aissa Abdelguerfi ◽

Meriem Laouar

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Cicer Arietinum ◽

Morphological Traits ◽

Ascochyta Blight ◽

Principal Component ◽

Breeding Programs ◽

Average Value ◽

Conservation Of Genetic Resources ◽

Resistant Genotypes

Assessment of genetic diversity among chickpea (Cicer arietinum L.) germplasm at the morphological and molecular levels is fundamental for chickpea breeding and conservation of genetic resources. Genetic variability of 46 chickpea genotypes including 42 Algerian genotypes and four control varieties was evaluated by using 15 agro-morphological traits. Eleven molecular markers including nine simple sequence repeats, one sequence characterised amplified region (SCY17) and one gene-specific (CaETR4) were used to characterise the 46 genotypes and eight references varieties added for disease resistance or susceptibility. Genotypes resistant to ascochyta blight were identified by the markers SCY17 and CaETR4 present together. High diversity was observed for all measured morphological traits between genotypes. Yield components, plant height, phenological traits and growth habit were the traits most involved in variation among genotypes and were partitioned into four groups by using principal component analysis. All molecular markers were polymorphic. In total, 91 alleles were obtained ranging from 2 to 21 per locus with average of 8.27 alleles per marker. Polymorphism information content ranged from 0.58 to 0.99 with an average value of 0.87. UPGMA clustering and Bayesian-based model structure analysis grouped genotypes into two clusters, but the distribution of the genotypes by cluster was not the same for the two analyses. According to the presence of markers indicating resistance to ascochyta blight (SCY17 and CaETR4), three resistant genotypes (FLIP 82-C92, ILC 6909, ILC 7241) were selected and should be tested in controlled conditions for confirmation. Considering the narrow diversity of cultivated chickpea, the Algerian genotypes can be considered as interesting for future breeding programs.

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Utilization of Molecular Marker Based Genetic Diversity Patterns in Hybrid Parents to Develop Better Forage Quality Multi-Cut Hybrids in Pearl Millet

Agriculture ◽

10.3390/agriculture9050097 ◽

2019 ◽

Vol 9 (5) ◽

pp. 97 ◽

Cited By ~ 2

Author(s):

Govintharaj Ponnaiah ◽

Shashi Kumar Gupta ◽

Michael Blümmel ◽

Maheswaran Marappa ◽

Sumathi Pichaikannu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Pearl Millet ◽

Morphological Traits ◽

Forage Quality ◽

Genotyping By Sequencing ◽

Single Nucleotide ◽

Breeding Programs ◽

Clear Cut

Genetic diversity of 130 forage-type hybrid parents of pearl millet was investigated based on multiple season data of morphological traits and two type of markers: SSRs (Simple sequence repeats) and GBS identified SNPs (Genotyping by sequencing-Single nucleotide polymorphism). Most of the seed and pollinator parents clustered into two clear-cut separate groups based on marker based genetic distance. Significant variations were found for forage related morphological traits at different cutting intervals (first and second cut) in hybrid parents. Across two cuts, crude protein (CP) varied from 11% to 15%, while in vitro organic matter digestibility (IVOMD) varied from 51% to 56%. Eighty hybrids evaluated in multi-location trial along with their parents for forage traits showed that significant heterosis can be realized for forage traits. A low but positive significant correlation found between SSR based genetic distance (GD between parents of hybrid) and heterosis for most of the forage traits indicated that SSR-based GD can be used for predicting heterosis for GFY, DFY and CP in pearl millet. An attempt was made to associate marker-based clusters with forage quality traits, to enable breeders select parents for crossing purposes in forage breeding programs.

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The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles

Frontiers in Plant Science ◽

10.3389/fpls.2020.569905 ◽

2020 ◽

Vol 11 ◽

Author(s):

Elisabetta Mazzucotelli ◽

Giuseppe Sciara ◽

Anna M. Mastrangelo ◽

Francesca Desiderio ◽

Steven S. Xu ◽

...

Keyword(s):

Genetic Diversity ◽

Durum Wheat ◽

Triticum Turgidum ◽

Snp Array ◽

Tetraploid Wheat ◽

Breeding Program ◽

Fixation Index ◽

Breeding Programs ◽

Genetic Clusters ◽

Modern Breeding

Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94–97% of the original diversity. The GDP consists of a wide representation of Triticum turgidum ssp. durum modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970–2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at r2 = 0.5. ADMIXTURE analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (k), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index (Fst) and diversity reduction index (DRI) metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology (Ppd and Vrn), plant height (Rht) and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.

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Structure and genetic diversity of Theobroma speciosum (Malvaceae) and implications for Brazilian Amazon conservation

Rodriguésia ◽

10.1590/2175-7860202172023 ◽

2021 ◽

Vol 72 ◽

Author(s):

Juliana de Freitas Encinas Dardengo ◽

Ana Aparecida Bandini Rossi ◽

Luiz Orlando de Oliveira ◽

Guilherme Ferreira Pena ◽

Luiz Henrique Rivas ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Molecular Genetic ◽

Economic Value ◽

Natural Populations ◽

Brazilian Amazon ◽

Fixation Index ◽

Breeding Programs ◽

Expected Heterozygosity ◽

Refuge Area

Abstract The genetic diversity of Theobroma speciosum is important because its use in breeding programs, once the species is closely related to species of great economic value such as Theobroma cacao (cocoa) and Theobroma grandiflorum (cupuaçu). Thus, the objective of this work is to characterize the intra and interpopulational genetic diversity of Theobroma speciosum in natural populations in the Brazilian Amazon. Ninety individuals of T. speciosum from four populations localized in different states of legal Amazon were selected and genotyped. The data were obtained by fluorescence microsatellite analysis and the number of alleles, number of private alleles, fixation index, observed and expected heterozygosity were analyzed. Bayesian analysis, AMOVA and PCOa were used to reveal the molecular genetic structure of the populations, using the programs Structure and GenAIEx 6.5, respectively. All populations studied present great levels of gene diversity, although, there was a greater similarity among the AUR, API and MAC populations, while RBC population presented higher heterozygosity and less inbreeding than the others, becoming a possible refuge area in the Amazon, and the most important population for T. speciosum conservation.

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Genetic diversity among wild and cultivated germplasm of the perennial pasture grass Phalaris aquatica, using DArTseq SNP marker analysis

Crop and Pasture Science ◽

10.1071/cp21112 ◽

2021 ◽

Vol 72 (10) ◽

pp. 823

Author(s):

Washington J. Gapare ◽

Andrzej Kilian ◽

Alan V. Stewart ◽

Kevin F. Smith ◽

Richard A. Culvenor

Keyword(s):

Genetic Diversity ◽

Middle Eastern ◽

Snp Markers ◽

Wild Germplasm ◽

Pasture Grass ◽

Additional Material ◽

Breeding Programs ◽

North West ◽

Phalaris Aquatica ◽

The Usa

Phalaris aquatica L. (phalaris) is a cool-season perennial grass originating from the Mediterranean Basin, north-west Africa and Middle Eastern regions that is used for livestock agriculture mainly in temperate areas with dry summers. It has been the subject of breeding programs in Australia, South America, New Zealand and the USA. Increased knowledge of relationships between wild and cultivated germplasm through use of molecular markers has the potential to facilitate future breeding gains. For this purpose, we conducted an analysis of P. aquatica by using 3905 polymorphic DArTseq SNP markers. Genetic diversity as measured by expected heterozygosity was similar for wild (HE = 0.14; n = 57) and cultivated (HE = 0.13; n = 37) accessions. Diversity in wild germplasm was generally continuous in nature, largely related to geographical location, with a division at the broadest scale into eastern and western clades, with more admixture in the western than the eastern clade. Structure analysis of wild germplasm indicated six subpopulations consistent with country of origin, with some admixture among subpopulations likely resulting from natural and human influences. There were nine subpopulations among wild and cultivated accessions combined. This population structure should be considered if genomic selection is applied in P. aquatica. Analysis of molecular variance indicated that 71% of the genetic variation occurred within subpopulations and 29% among subpopulations. Genetic distances were low among cultivated germplasm from most countries except the USA, which was more distinct. Evaluation of material from the US pool by breeding programs in other countries, and additional material from the less utilised eastern clade, may be worthwhile.

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AGRO-MORPHOLOGICAL CHARACTERIZATION AND GENETIC DIVERSITY OF GUARANA CULTIVARS

BRAZILIAN JOURNAL OF AGRICULTURE - Revista de Agricultura ◽

10.37856/bja.v94i3.3561 ◽

2019 ◽

Vol 94 (3) ◽

pp. 166

Author(s):

Pablo Roberto da Silva Ozorio ◽

André Luiz Atroch ◽

Firmino José do Nascimento Filho

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Morphological Traits ◽

Agronomic Traits ◽

Morphological Characterization ◽

High Variability ◽

Great Variability ◽

Breeding Programs ◽

High Genetic Variability ◽

Superior Genotypes

Based on agro-morphological traits, this study aimed to describe and quantify the genetic diversity between eighteen guarana cultivars from the guarana breeding program, to identify cultivars for use in multiple-purpose in breeding programs to obtain segregating populations with great variability and diversity. Dis-similarity between cultivars was calculated using Gower’s algorithm and a dendrogram was obtained using the UPGMA algorithm. High genetic variability and diversity was identified between guarana cultivars via 20 morpho-agronomic traits. Two groups and six subgroups of genetic diversity were identified. Crosses between clones of different subgroups may produce high variability and diversity in segregating populations, increasing the capacity to select for superior genotypes in these populations.

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PROFILING OF GUAVA GENOTYPES GROWN IN VIDARBHA CONDITIONS ON THE BASIS OF MORPHOLOGICAL TRAITS

FLORA AND FAUNA ◽

10.33451/florafauna.v23i1pp37-44 ◽

2017 ◽

Vol 23 (1) ◽

Author(s):

R.A. PATIL ◽

S.G. BHARAD ◽

S.N. SAWANT

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Morphological Traits ◽

Considerable Extent ◽

Fruit Traits ◽

Breeding Programmes ◽

Tree Leaf ◽

Qualitative Characteristics ◽

Intrapopulation Diversity

Assessment of genetic diversity in the available germplasm is the prerequisite for development of improved genotypes through planned breeding programmes. In the view of this Forty-eight genotypes of seedling origin guava along with 1 check (L-49/Sardar) collected and conserved at germplasm block, Main Garden, Department of Horticulture, Dr. P. D. A. University, Akola were evaluated for genetic variability and diversity based on the qualitative characteristics. The genotypes were evaluated for sixteen morphological traitsviz. tree, leaf, floral and fruit traits. Results Show considerable extent of variability amongst the 49 genotypes in each traits. A sizeable amount of intrapopulation diversity recorded can be used to identify diverse parents which can be utilized in hybridization programmes.

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Combining metabolomic and transcriptomic approaches to assess and improve crop quality traits

CABI Agriculture and Bioscience ◽

10.1186/s43170-020-00021-8 ◽

2021 ◽

Vol 2 (1) ◽

Author(s):

Delphine M. Pott ◽

Sara Durán-Soria ◽

Sonia Osorio ◽

José G. Vallarino

Keyword(s):

Quality Trait ◽

Quality Traits ◽

Crop Species ◽

Breeding Programs ◽

Crop Quality ◽

Crop Varieties ◽

New Genes ◽

Technical Advances ◽

Health Promoting ◽

Selection Of

AbstractPlant quality trait improvement has become a global necessity due to the world overpopulation. In particular, producing crop species with enhanced nutrients and health-promoting compounds is one of the main aims of current breeding programs. However, breeders traditionally focused on characteristics such as yield or pest resistance, while breeding for crop quality, which largely depends on the presence and accumulation of highly valuable metabolites in the plant edible parts, was left out due to the complexity of plant metabolome and the impossibility to properly phenotype it. Recent technical advances in high throughput metabolomic, transcriptomic and genomic platforms have provided efficient approaches to identify new genes and pathways responsible for the extremely diverse plant metabolome. In addition, they allow to establish correlation between genotype and metabolite composition, and to clarify the genetic architecture of complex biochemical pathways, such as the accumulation of secondary metabolites in plants, many of them being highly valuable for the human diet. In this review, we focus on how the combination of metabolomic, transcriptomic and genomic approaches is a useful tool for the selection of crop varieties with improved nutritional value and quality traits.

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