Assessment of genetic diversity of rice based on SNP markers for selection of parents for sheath rot (Sarocladium oryzae) resistance breeding

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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Revealing the genetic diversity of wheat varieties (lines) in China based on SNP markers

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2020.91039 ◽

2019 ◽

Vol 46 (2) ◽

pp. 307-314

Author(s):

Yu-Qing ZHANG ◽

Juan ZOU ◽

Yi-Ke LIU ◽

Wei-Jie HE ◽

Zhan-Wang ZHU ◽

...

Keyword(s):

Genetic Diversity ◽

Snp Markers ◽

Wheat Varieties

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Genetic Similarity of Avena sativa L. Varieties as an Example of a Narrow Genetic Pool of Contemporary Cereal Species

Plants ◽

10.3390/plants10071424 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1424

Author(s):

Magdalena Cieplak ◽

Sylwia Okoń ◽

Krystyna Werwińska

Keyword(s):

Genetic Diversity ◽

Avena Sativa ◽

Genetic Similarity ◽

Breeding Programs ◽

Central European ◽

Cereal Species ◽

Genetic Pool ◽

Selection Of ◽

High Genetic Similarity

The assessment of the genetic diversity of cultivated varieties is a very important element of breeding programs. This allows the determination of the level of genetic differentiation of cultivated varieties, their genetic distinctiveness, and is also of great importance in the selection of parental components for crossbreeding. The aim of the present study was to determine the level of genetic diversity of oat varieties currently grown in Central Europe based on two marker systems: ISSR and SCoT. The research conducted showed that both these types of markers were suitable for conducting analyses relating to the assessment of genetic diversity. The calculated coefficients showed that the analyzed cultivars were characterized by a high genetic similarity. However, the UPGMA and PCoA analyses clearly indicated the distinctiveness of the breeding programs conducted in Central European countries. The high genetic similarity of the analyzed forms allow us to conclude that it is necessary to expand the genetic pool of oat varieties. Numerous studies show that landraces may be the donor of genetic variation.

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Genetic diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium falciparum on Bioko Island, Equatorial Guinea and global comparative analysis

Malaria Journal ◽

10.1186/s12936-021-03664-8 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Li-Yun Lin ◽

Hui-Ying Huang ◽

Xue-Yan Liang ◽

Dong-De Xie ◽

Jiang-Tao Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Natural Selection ◽

Protein Structure ◽

Transmembrane Protein ◽

Fixation Index ◽

Bioko Island ◽

Adhesive Protein ◽

Trap Gene ◽

Selection Of

Abstract Background Thrombospondin-related adhesive protein (TRAP) is a transmembrane protein that plays a crucial role during the invasion of Plasmodium falciparum into liver cells. As a potential malaria vaccine candidate, the genetic diversity and natural selection of PfTRAP was assessed and the global PfTRAP polymorphism pattern was described. Methods 153 blood spot samples from Bioko malaria patients were collected during 2016–2018 and the target TRAP gene was amplified. Together with the sequences from database, nucleotide diversity and natural selection analysis, and the structural prediction were preformed using bioinformatical tools. Results A total of 119 Bioko PfTRAP sequences were amplified successfully. On Bioko Island, PfTRAP shows its high degree of genetic diversity and heterogeneity, with π value for 0.01046 and Hd for 0.99. The value of dN–dS (6.2231, p < 0.05) hinted at natural selection of PfTRAP on Bioko Island. Globally, the African PfTRAPs showed more diverse than the Asian ones, and significant genetic differentiation was discovered by the fixation index between African and Asian countries (Fst > 0.15, p < 0.05). 667 Asian isolates clustered in 136 haplotypes and 739 African isolates clustered in 528 haplotypes by network analysis. The mutations I116T, L221I, Y128F, G228V and P299S were predicted as probably damaging by PolyPhen online service, while mutations L49V, R285G, R285S, P299S and K421N would lead to a significant increase of free energy difference (ΔΔG > 1) indicated a destabilization of protein structure. Conclusions Evidences in the present investigation supported that PfTRAP gene from Bioko Island and other malaria endemic countries is highly polymorphic (especially at T cell epitopes), which provided the genetic information background for developing an PfTRAP-based universal effective vaccine. Moreover, some mutations have been shown to be detrimental to the protein structure or function and deserve further study and continuous monitoring.

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Molecular and phylogenetic analysis reveals new diversity of Dunaliella salina from hypersaline environments

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315420001319 ◽

2021 ◽

pp. 1-11

Author(s):

Andrea Highfield ◽

Angela Ward ◽

Richard Pipe ◽

Declan C. Schroeder

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Dunaliella Salina ◽

Phylogenetic Analyses ◽

Ssu Rdna ◽

Lsu Rdna ◽

Hypersaline Environments ◽

Rdna Its ◽

Β Carotene ◽

Selection Of

Abstract Twelve hyper-β carotene-producing strains of algae assigned to the genus Dunaliella salina have been isolated from various hypersaline environments in Israel, South Africa, Namibia and Spain. Intron-sizing of the SSU rDNA and phylogenetic analysis of these isolates were undertaken using four commonly employed markers for genotyping, LSU rDNA, ITS, rbcL and tufA and their application to the study of Dunaliella evaluated. Novel isolates have been identified and phylogenetic analyses have shown the need for clarification on the taxonomy of Dunaliella salina. We propose the division of D. salina into four sub-clades as defined by a robust phylogeny based on the concatenation of four genes. This study further demonstrates the considerable genetic diversity within D. salina and the potential of genetic analyses for aiding in the selection of prospective economically important strains.

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Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

Plant Genetic Resources ◽

10.1017/s1479262121000034 ◽

2021 ◽

Vol 19 (1) ◽

pp. 20-28

Author(s):

Abush Tesfaye Abebe ◽

Adesike Oladoyin Kolawole ◽

Nnanna Unachukwu ◽

Godfree Chigeza ◽

Hailu Tefera ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Glycine Max ◽

Snp Markers ◽

Fixation Index ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Breeding Lines ◽

Soybean Germplasm ◽

Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

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All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

Diversity ◽

10.3390/d13040139 ◽

2021 ◽

Vol 13 (4) ◽

pp. 139

Author(s):

Marlien M. van der Merwe ◽

Jia-Yee S. Yap ◽

Peter D. Wilson ◽

Helen T. Murphy ◽

Andrew Ford

Keyword(s):

Genetic Diversity ◽

Allelic Variation ◽

Germplasm Conservation ◽

Snp Markers ◽

Genomic Diversity ◽

Ex Situ ◽

Spatial Distance ◽

Genetic Connectivity ◽

Conservation Genomics ◽

Modelling Framework

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

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Genetic diversity and selection of genotypes to enhance Zn and Fe content in common bean

Canadian Journal of Plant Science ◽

10.4141/cjps09096 ◽

2010 ◽

Vol 90 (1) ◽

pp. 49-60 ◽

Cited By ~ 13

Author(s):

Z I Talukder ◽

E Anderson ◽

P N Miklas ◽

M W Blair ◽

J Osorno ◽

...

Keyword(s):

Genetic Diversity ◽

Common Bean ◽

Allelic Variation ◽

Gene Pools ◽

Gene Sequences ◽

Mineral Contents ◽

Discriminatory Ability ◽

Fe Content ◽

Mapping Populations ◽

Selection Of

Common bean (Phaseolus vulgaris L.) is an important source of dietary protein and minerals worldwide. Genes conditioning variability for mineral contents are not clearly understood. Our ultimate goal is to identify genes conditioning genetic variation for Zn and Fe content. To establish mapping populations for this objective, we tested mineral content of 29 common bean genotypes. Chemical analyses revealed significant genetic variability for seed Zn and Fe contents among the genotypes. Genetic diversity was evaluated with 49 primer pairs, of which 23 were simple sequence repeats (SSR), 16 were developed from tentative consensus (TC) sequences, and 10 were generated from common bean NBS-LRR gene sequences. The discriminatory ability of molecular markers for identifying allelic variation among genotypes was estimated by polymorphism information content (PIC) and the genetic diversity was measured from genetic similarities between genotypes. Primers developed from NBS-LRR gene sequences were highly polymorphic in both PIC values and number of alleles (0.82 and 5.3), followed by SSRs (0.56 and 3.0), and markers developed from TC (0.39 and 2.0). genetic similarity values between genotypes ranged from 14.0 (JaloEEP558 and DOR364) to 91.4 (MIB152 and MIB465). Cluster analysis clearly discriminated the genotypes into Mesoamerican and Andean gene pools. Common bean genotypes were selected to include in crossing to enhance seed Zn and Fe content based on genetic diversity and seed mineral contents of the genotypes. Key words: Common bean, genetic diversity, mineral nutrients, breeding

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Machine learning, transcriptome, and genotyping chip analyses provide insights into SNP markers identifying flower color in Platycodon grandiflorus

Scientific Reports ◽

10.1038/s41598-021-87281-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Go-Eun Yu ◽

Younhee Shin ◽

Sathiyamoorthy Subramaniyam ◽

Sang-Ho Kang ◽

Si-Myung Lee ◽

...

Keyword(s):

Machine Learning ◽

Random Forest ◽

Feature Selection Method ◽

Flower Color ◽

Classification Performance ◽

Snp Markers ◽

Rna Seq ◽

Color Classification ◽

Dna Pcr ◽

Selection Of

AbstractBellflower is an edible ornamental gardening plant in Asia. For predicting the flower color in bellflower plants, a transcriptome-wide approach based on machine learning, transcriptome, and genotyping chip analyses was used to identify SNP markers. Six machine learning methods were deployed to explore the classification potential of the selected SNPs as features in two datasets, namely training (60 RNA-Seq samples) and validation (480 Fluidigm chip samples). SNP selection was performed in sequential order. Firstly, 96 SNPs were selected from the transcriptome-wide SNPs using the principal compound analysis (PCA). Then, 9 among 96 SNPs were later identified using the Random forest based feature selection method from the Fluidigm chip dataset. Among six machines, the random forest (RF) model produced higher classification performance than the other models. The 9 SNP marker candidates selected for classifying the flower color classification were verified using the genomic DNA PCR with Sanger sequencing. Our results suggest that this methodology could be used for future selection of breeding traits even though the plant accessions are highly heterogeneous.

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