Genome diversity and population structure analysis of Iranian landrace and improved barley (Hordeum vulgare L.) genotypes using arbitrary functional gene-based molecular markers

The objective of this study was to evaluate the genetic diversity of the Colombian Creole donkey in the Department of Sucre using Random Amplified Microsatellites (RAM) molecular markers. In 100 individuals from the five subregions of the department, DNA was extracted and five RAM primers were amplified by PCR. In all, 291 bands were found, on average 11.96±1.45 per primer, the highest value in CCA (18±2.23) and the lowest in TG and GT (8.8±0.44). CA was the most polymorphic primer (88.09±10.91%) with the highest heterozygosity value (He) (0.376±0.021), while the lowest was GT (0.341±0.076 and 0.101±0.040, respectively). Intrapopulation analysis showed an average of 66.50±1.72 bands, of which 89.86±24.04% were polymorphic. The highest number of bands (63±3.84) was found in the Gulf of Morrosquillo (GO) subpopulation, and the lowest in Mojana (MO) (48±2.88); however, the highest value of polymorphic loci (81.16%) and He (0.335±0.022) were found in the Montes de María (MM) subpopulation, making it the most diverse. The average genetic diversity for the entire population was 0.351±0.021 bands. The population structure analysis showed a 10% variation between subpopulations, with an FST value of 0.17±0.01 (P<0.05). Genetic distances between subpopulations showed that MO and GO were the most distant. The RAM markers are effective in assessing the genetic diversity of the Creole donkey, which has high values of genetic diversity, particularly the MM subpopulation. The genetic revealed structure could be the result of natural geographical barriers between the subregions.

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Characterization of pepper accessions using molecular markers linked to pungency and SSR

Horticultura Brasileira ◽

10.1590/s0102-053620190205 ◽

2019 ◽

Vol 37 (2) ◽

pp. 152-160

Author(s):

Rafaela de Jesus ◽

Gabriel do N Santos ◽

Andressa S Piccin ◽

Thiago WA Balsalobre ◽

Fernando C Sala ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Microsatellite Markers ◽

Structure Analysis ◽

Breeding Programs ◽

Population Structure Analysis ◽

Level Information ◽

Capsicum Spp ◽

Genus Capsicum

ABSTRACT Peppers of the genus Capsicum are of great socioeconomic importance, being pungency trait their main attraction. Pungency characterization, genetic distance estimates and population structure analysis of the accessions belonging to germplasm banks are important for parent selection which allows to obtain superior progenies. Therefore, the aims of this study were: i) evaluate 81 accessions of the Capsicum spp. Germplasm Bank of Universidade Federal de São Carlos (BGC-UFSCar) with molecular markers linked to pungency; ii) estimate the genetic diversity among accessions of the BGC-UFSCar using microsatellite markers (SSR); and iii) evaluate the efficiency of these markers in the distinction among species of Capsicum spp. We noticed that pun11 and SNP molecular markers were efficient in predicting the pungent phenotype of BGC-UFSCar accessions in 84.85% and 95.59%, respectively. From a total of 13 amplified microsatellite markers, seven were polymorphic and efficient to discriminate species of Capsicum genus, both through genetic diversity analysis and population structure analysis, which showed three subpopulations. The molecular markers used in this study are useful tools for breeding programs since they were able to characterize and discriminate Capsicum spp. species at DNA level. Information obtained with molecular markers can assist in the selection of contrasting parents for future breeding programs.

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Genetic diversity assessment and population structure analysis of pomegranate cultivars from different countries and Himalayan wild accessions

The Journal of Horticultural Science and Biotechnology ◽

10.1080/14620316.2021.1899854 ◽

2021 ◽

pp. 1-10

Author(s):

Raghavendra Gunnaiah ◽

Rudrappa C. Jagadeesha ◽

Sarvamangala Cholin ◽

Guranna Prabhuling ◽

Ammanaghatta Govindaswamy Babu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Structure Analysis ◽

Population Structure Analysis ◽

Diversity Assessment ◽

Wild Accessions

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Genetic Diversity and Population Structure of Serbian Barley (Hordeum vulgare L.) Collection during a 40-Year Long Breeding Period

Agronomy ◽

10.3390/agronomy11010118 ◽

2021 ◽

Vol 11 (1) ◽

pp. 118

Author(s):

Ljiljana Brbaklić ◽

Dragana Trkulja ◽

Sanja Mikić ◽

Milan Mirosavljević ◽

Vojislava Momčilović ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Hordeum Vulgare ◽

Crop Improvement ◽

Genetic Erosion ◽

Breeding Period ◽

Phenotypic Variance ◽

Hordeum Vulgare L ◽

Phenotypic Data ◽

Breeding Material

Determination of genetic diversity and population structure of breeding material is an important prerequisite for discovering novel and valuable alleles aimed at crop improvement. This study’s main objective was to characterize genetic diversity and population structure of a collection representing a 40-year long historical period of barley (Hordeum vulgare L.) breeding, using microsatellites, pedigree, and phenotypic data. The set of 90 barley genotypes was phenotyped during three growing seasons and genotyped with 338 polymorphic alleles. The indicators of genetic diversity showed differentiation changes throughout the breeding periods. The population structure discriminated the breeding material into three distinctive groups. The principal coordinate analysis grouped the genotypes according to their growth habit and row type. An analysis of phenotypic variance (ANOVA) showed that almost all investigated traits varied significantly between row types, seasons, and breeding periods. A positive effect on yield progress during the 40-year long breeding period could be partly attributed to breeding for shorter plants, which reduced lodging and thus provided higher yield stability. The breeding material revealed a considerable diversity level based on microsatellite and phenotypic data without a tendency of genetic erosion throughout the breeding history and implied dynamic changes in genetic backgrounds, providing a great gene pool suitable for further barley improvement.

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Genetic diversity and population structure analysis of Lateolabrax maculatus from Chinese coastal waters using polymorphic microsatellite markers

Scientific Reports ◽

10.1038/s41598-021-93000-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Wei Wang ◽

Chunyan Ma ◽

Longling Ouyang ◽

Wei Chen ◽

Ming Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Structure Analysis ◽

Principal Component ◽

Genetic Constitution ◽

Southern Group ◽

Population Structure Analysis ◽

Lateolabrax Maculatus ◽

Geographic Populations ◽

Geographic Separation

AbstractIn order to provide valuable guidelines for the conservation of germplasm of Lateolabrax maculatus, the genetic diversity and population structure analysis were evaluated for eight geographic populations along coastal regions of China, using 11 microsatellite DNA markers. The genetic parameters obtained showed that, eight populations can be clustered into two groups, the Northern group and the Southern group, concordant with their geographical positions. The UPGMA tree constructed according to the Nei’s genetic distance along with the structure analysis and discriminant analysis of principal component also supported this result. This might be explained by the geographic separation and the divergent environmental conditions among the populations. It's worth noting that, QD (Qingdao) population from northern area was assigned to the Southern group and showed a close genetic relationship and similar genetic constitution with the southern populations. We speculated that large scales of anthropogenic transportation of wild fries from QD populations to the southern aquaculture areas in history should be the primary cause. The populations from GY (Ganyu), RD (Rudong) and BH (Binhai) had higher genetic diversity and showed limited genetic exchange with other populations, indicating better conservation of the natural resources in these regions. All populations were indicated to have experienced bottleneck events in history.

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