Genetic diversity computation in sesame genotypes using morphological traits and genic SSR markers

Sesame (Sesamum indicum L.), the most ancient and important oilseed crop, with rich source of protein, highquality seed oil and many antioxidant properties is extensively grown in India. In the present study, 235 genic markers developed through data mining of expressed sequence tags from the NCBI database were used to assess the molecular genetic diversity at molecular level of 70 genotypes, belonging to different eco-geographical regions of the world. Of the developed markers, 35 (15%) showed polymorphism with a total of 151 alleles identified across genotypes. The alleles detected by the markers varied from 3 to 6 with an average of 4.36 along with 69% of average genetic diversity. The polymorphic information content (PIC) ranged from 0.36 to 0.82, with an average of 0.61. Neighbor-Joining (NJ) analysis revealed the five major groups, and clustering was independent to geographic origin. By using UPGMA, 70 genotypes at 70% similarity coefficient among the morphological traits were classified into four distinct clusters and the clustering pattern was different than based on molecular markers.

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Molecular genetic diversity and conservation priorities of Egyptian rabbit breeds

World Rabbit Science ◽

10.4995/wrs.2019.8923 ◽

2019 ◽

Vol 27 (3) ◽

pp. 135

Author(s):

O.A.M. Badr ◽

I.I.S. El-Shawaf ◽

M.H.A. Khalil ◽

M.H. Refaat ◽

S.I.A. Ramadan

Keyword(s):

Genetic Diversity ◽

Information Content ◽

Polymorphic Information Content ◽

Molecular Genetic ◽

Vital Role ◽

Conservation Priorities ◽

Molecular Genetic Diversity ◽

Hardy Weinberg Equilibrium ◽

Diversity Studies ◽

Nei's Genetic Distance

<p>The limited rabbit resources in Egypt are threatened by the danger of extinction, whereas genetic diversity studies of native breeds could play a vital role in conservation and improvement of these breeds. In this study, 3 native rabbit breeds: Gabali (G), Baladi Red (BR) and Baladi Black (BB), in addition to New Zealand White (NZW), were genotyped using 12 microsatellite markers. All the typed microsatellites were polymorphic by average number of alleles 5.25 per locus. Observed and expected heterozygosity per locus averaged 0.62 and 0.68, respectively. The average polymorphic information content was 0.71 and the highest polymorphic information content was recorded in locus SOL33 by 0.85. All the studied loci except SAT7 and SAT2 showed deviation from Hardy-Weinberg equilibrium with significant level. The inbreeding coefficient of the individuals relative to the total population was 0.07. The within-population heterozygote deficit averaged 0.07 and ranged from 0.141 in BR to 0.015 in BB breeds. The highest pairwise differentiation among the populations was recorded between BB and NZW (0.071), while the lowest value was recorded between BR and both of G (0.038) and BB (0.039). The lowest pairwise Nei’s genetic distance was recorded between BR and BB (0.190), while the highest was recorded between NZW and BB breeds (0.409). BR and G populations were clustered together forming an admixed mosaic cluster. BR recorded the highest contribution in the aggregate genetic diversity based on the three prioritisation methods used.</p>

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Analysis of Morphological and Molecular Genetic Diversity of Salicornia Iranica Akhani Wildlife Populations around Urmia Lake, Iran

10.21203/rs.3.rs-584493/v1 ◽

2021 ◽

Author(s):

Mohammad Aghaei ◽

Abbas Hassani ◽

Hossein Nazemiyeh ◽

Babak Abdollahi Mandoulakani ◽

Mohammad Saadatian

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Morphological Traits ◽

Molecular Genetic ◽

Morphological Diversity ◽

Molecular Data ◽

Issr Markers ◽

Shannon Index ◽

Urmia Lake ◽

Molecular Genetic Diversity

Abstract Salicornia is a halophyte plant capable of being irrigated with seawater, which can be used as an alternative food. Given this, it is necessary to study the potentials of this plant's morphological diversity in the natural environment. In this study, 33 wild populations of Salicornia were collected from different geographical areas around Urmia Lake during the flowering stage, and some morphological traits and 25 ISSR loci of the plant were measured. Based on morphological traits and the cluster analysis, Salicornia populations were divided into four groups. Overall, the high percentage of polymorphic gene loci (65.69%), the average number of effective alleles per gene locus (1.63), and the Shannon data index (0.540) indicate that ISSR markers can be used in Identify genetic diversity to be used. Molecular data cluster analysis divided the studied populations into two main groups, which included 12.12% and 87.88% of the populations, respectively. Based on the effective analysis of the population's genetic structure and the precise classification of individuals into suitable sub-populations, the value of K = 2 was calculated. The research findings indicated that markers UBC823, B, A7, and K, and with the Shannon index, effective allele, and large heterozygosity values are markers with the highest effectiveness compared to other markers utilized, and they are used better than other compounds in genetic distance. The findings of this study will aid in parental selection studies for breeding programs of salicornia in future.

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Molecular genetic diversity and linked resistance to ascochyta blight in Australian chickpea breeding materials and their wild relatives

Australian Journal of Agricultural Research ◽

10.1071/ar07386 ◽

2008 ◽

Vol 59 (6) ◽

pp. 554 ◽

Cited By ~ 14

Author(s):

M. Imtiaz ◽

M. Materne ◽

K. Hobson ◽

M. van Ginkel ◽

R. S. Malhotra

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genetic Similarity ◽

Polymorphic Information Content ◽

Molecular Genetic ◽

Ascochyta Blight ◽

Wild Relatives ◽

Pedigree Information ◽

Common Source ◽

Molecular Genetic Diversity

Simple sequence-repeat (SSR) and sequence characterised amplified regions (SCARs) have been used to characterise the genetic diversity of chickpea germplasm. A set of 48 genotypes comprising cultigen, landraces, and wild relatives important for breeding purposes was used to determine the genetic similarity between genotypes and to assess the association between ascochyta blight (AB) and SCAR phenotypes. The 21 SSR markers amplified a total of 370 alleles, with an average of ~17 alleles per SSR locus among the 48 genotypes. Polymorphic information content (PIC) values ranged from 0.37 for the XGA13 locus to 0.93 for the XGA106. Principal coordinate analysis (PCO) of genetic similarity (GS) estimates revealed a clear differentiation of the chickpea genotypes into 5 groups, which were generally consistent with available pedigree information. Comparison of SCAR and AB phenotypes enabled us to tag the common source(s) of AB resistance in the breeding collection. Based on the SCAR phenotypes, it was evident that the studied chickpea genotypes, including worldwide-known AB-resistant lines (ICC12004, ILC72, ILC3279), carry at least one common source of resistance to AB. Since SSR markers are polymerase chain reaction (PCR)-based markers, highly polymorphic, and amenable to high-throughput technologies, they are therefore well suited for studies of genetic diversity and cultivar identification in chickpea. The broad level of genetic diversity detected in the chickpea germplasm should be useful for selective breeding for specific traits such as AB, backcrossing, and in enhancing the genetic base of breeding programs.

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ANALISIS KERAGAMAN GENETIK AKSESI KEDELAI INTRODUKSI DARI WILAYAH SUBTROPIS BERBASIS MORFOLOGI DAN MOLEKULER

BERITA BIOLOGI ◽

10.14203/beritabiologi.v19i3b.3894 ◽

2020 ◽

Vol 19 (3B) ◽

Author(s):

Rerenstradika Tizar Terryana ◽

Nickita Dewi Safina ◽

Suryani Suryani ◽

Kristianto Nugroho ◽

Puji Lestari

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Molecular Genetic ◽

Flower Color ◽

Morphological Characters ◽

Breeding Program ◽

United States Department ◽

Average Value ◽

Molecular Genetic Diversity

Genetic diversity information on soybean germplasm will establish the success of soybean breeding program. In the present study, four qualitative morphological traits information collected from Germplasm Resources Information Network (GRIN), United States Department of Agriculture (USDA) database (www.ars-grin.gov) and 10 microsatellite markers were used to analyze the relationship among 45 accessions of subtropical introduced soybean. The morphological characters of introduced soybean accessions contributed to support the result of molecular characterization. The introduced soybean accessions used in this study were diverse based on morphological and molecular characters. Based on principle component analysis, the flower color, pod color, and growth habit contributed most of the total genetic diversity. All introduced accessions were overlap into four quadrants based on principal coordinate analysis. All microsatellite primers showed polymorphism on total accession observed. High allele variation (9–27 alleles) was observed among tested accessions, with an average allele number and Polymorphic Information Content (PIC) value of 20.7 and 0.95 (0.92–0.97), respectively. All microsatellite markers showed PIC value >0.7 indicating that these markers were suitable for soybean diversity studies with high differentiation and with the average value of genetic diversity of 0.95. The phylogenetic analysis revealed that 45 soybean accessions could be divided into two major groups. Soybean accessions belonging to the same area did not always occupy the same group. The results confirmed that both morphology and molecular genetic diversity in a combined way could efficiently evaluate the variation present in different soybean accessions in any breeding program.

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