Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations

The chicken major histocompatibility complex (MHC) on chromosome 16 is the most polymorphic region across the whole genome, and also an ideal model for genetic diversity investigation. The MHC B-F/B-L region is 92 kb in length with high GC content consisting of 18 genes and one pseudogene (Blec4), which plays important roles in immune response. To evaluate polymorphism of the Chinese indigenous chickens as well as to analyze the effect of selection to genetic diversity, we used WaferGen platform to identify sequence variants of the B-F/B-L region in 21 chicken populations, including the Red Jungle Fowl (RJF), Cornish (CS), White Leghorns (WLs), 16 Chinese domestic breeds, and two well-known inbred lines 63 and 72. A total of 3,319 single nucleotide polymorphism (SNPs) and 181 INDELs in the B-F/B-L region were identified among 21 populations, of which 2,057 SNPs (62%) and 159 INDELs (88%) were novel. Most of the variants were within the intron and the flanking regions. The average variation density was 36 SNPs and 2 INDELs per kb, indicating dramatical high diversity of this region. Furthermore, BF2 was identified as the hypervariable genes with 67 SNPs per kb. Chinese domestic populations showed higher diversity than the WLs and CS. The indigenous breeds, Nandan Yao (NY), Xishuangbanna Game (XG), Gushi (GS), and Xiayan (XY) chickens, were the top four with the highest density of SNPs and INDELs. The highly inbred lines 63 and 72 have the lowest diversity, which might be resulted from a long-term intense selection for decades. Collectively, we refined the genetic map of chicken MHC B-F/B-L region, and illustrated genetic diversity of 21 chicken populations. Abundant genetic variants were identified, which not only strikingly expanded the current Ensembl SNP database, but also provided comprehensive data for researchers to further investigate association between variants in MHC and immune traits.

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MOLECULAR CHARACTERIZATION AND DIVERSITY ANALYSIS OF SELECTED MAIZE INBRED LINES USING SINGLE NUCLEOTIDE POLYMORPHISM MARKERS

Canadian Journal of Plant Science ◽

10.1139/cjps-2020-0051 ◽

2020 ◽

Author(s):

Mwaikonyole Zawadi ◽

Julia Sibiya ◽

Kingstone Mashingaidze ◽

Assefa B Amelework ◽

Aleck Kondwakwenda ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Agricultural Research ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Inbred Lines ◽

Nucleotide Polymorphism ◽

Heterotic Groups ◽

Single Nucleotide ◽

Maize Inbred Lines

The level of genetic diversity among the available breeding materials determines the potential success of a breeding program. In this study, 92 maize inbred lines were genotyped with 3047 single nucleotide polymorphism (SNP) markers using a Kompetitive Allele-Specific Polymerase chain reaction (KASPTM) genotyping protocol. The objectives were to determine the level and pattern of genetic diversity and define potential heterotic groups of maize inbred lines developed by the Agricultural Research Council maize program of South Africa. More than 91% of the SNPs used were polymorphic with mean polymorphic information content (PIC) of 0.36. Gene diversity ranged from 0.35 to 0.37, with a mean of 0.36. Cluster analysis revealed the presence of three distinct subpopulations. Analysis of molecular variance revealed low but highly significant (p<0.0001) variations among populations, high within and among individual variations. Variation among individuals contributed 83% of the total variation, whereas variation within individuals and among populations contributed 14% and 3%, respectively. Low mean population differentiation observed in this study suggested that the inbred lines might be developed from parental genotypes with similar genetic backgrounds. The mean percentage of genetic purity among the inbred lines was 4.8, with more than 79% of the inbred lines exhibiting less than 5% heterozygosity, indicating the inbred lines are fixed. Genotypes in different clusters may be earmarked as belonging to distinct heterotic groups, and their crosses may result in better heterosis. Thus, the findings of this study set the basis for earmarking heterotic groups and parental selection.

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Genetic diversity among INERA maize inbred lines with single nucleotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines

BMC Genetics ◽

10.1186/s12863-014-0127-2 ◽

2014 ◽

Vol 15 (1) ◽

Cited By ~ 14

Author(s):

Abdalla Dao ◽

Jacob Sanou ◽

Sharon E Mitchell ◽

Vernon Gracen ◽

Eric Y Danquah

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Inbred Lines ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Maize Inbred Lines

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Genetic Diversity of Purple Passion Fruit, Passiflora edulis f. edulis, Based on Single-Nucleotide Polymorphism Markers Discovered through Genotyping by Sequencing

Diversity ◽

10.3390/d13040144 ◽

2021 ◽

Vol 13 (4) ◽

pp. 144

Author(s):

Nohra Castillo Rodríguez ◽

Xingbo Wu ◽

María Isabel Chacón ◽

Luz Marina Melgarejo ◽

Matthew Wohlgemuth Blair

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Genotyping By Sequencing ◽

Passion Fruit ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Passiflora Edulis ◽

Tropical Fruit ◽

Commercial Cultivars ◽

Purple Passion Fruit

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.

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The Evolution of Isochores: Evidence From SNP Frequency Distributions

Genetics ◽

10.1093/genetics/162.4.1805 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1805-1810 ◽

Cited By ~ 1

Author(s):

Martin J Lercher ◽

Nick G C Smith ◽

Adam Eyre-Walker ◽

Laurence D Hurst

Keyword(s):

Population Genetics ◽

Large Scale ◽

Gc Content ◽

Nucleotide Composition ◽

Compositional Variation ◽

Mutation Bias ◽

Single Nucleotide ◽

Frequency Distributions ◽

Noncoding Regions ◽

Standard Population

AbstractThe large-scale systematic variation in nucleotide composition along mammalian and avian genomes has been a focus of the debate between neutralist and selectionist views of molecular evolution. Here we test whether the compositional variation is due to mutation bias using two new tests, which do not assume compositional equilibrium. In the first test we assume a standard population genetics model, but in the second we make no assumptions about the underlying population genetics. We apply the tests to single-nucleotide polymorphism data from noncoding regions of the human genome. Both models of neutral mutation bias fit the frequency distributions of SNPs segregating in low- and medium-GC-content regions of the genome adequately, although both suggest compositional nonequilibrium. However, neither model fits the frequency distribution of SNPs from the high-GC-content regions. In contrast, a simple population genetics model that incorporates selection or biased gene conversion cannot be rejected. The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions.

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Development of a core set of single nucleotide polymorphism markers for genetic diversity analysis and cultivar fingerprinting in cowpea

Legume Science ◽

10.1002/leg3.93 ◽

2021 ◽

Author(s):

Xinyi Wu ◽

Baogen Wang ◽

Suqi Wu ◽

Sujuan Li ◽

Yan Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Diversity Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Genetic Diversity Analysis ◽

Core Set

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SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity

Virus Evolution ◽

10.1093/ve/veab013 ◽

2021 ◽

Author(s):

Juliana D Siqueira ◽

Livia R Goes ◽

Brunna M Alves ◽

Pedro S de Carvalho ◽

Claudia Cicala ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Cancer Patients ◽

Disease Severity ◽

Healthcare Workers ◽

Viral Population ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Consensus Sequences ◽

Vulnerable Patients

Abstract Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (non-cancer controls) by deep sequencing and investigated the within-host viral population of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers from the Brazilian National Cancer Institute were collected in April–May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%) among the consensus sequences. Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to healthcare workers. This difference was independent of SARS-CoV-2 Ct values obtained at the diagnostic tests, which did not differ between the two groups. The most common nucleotide changes of intrahost SNVs in both groups were consistent with APOBEC and ADAR activities. Intrahost genetic diversity in cancer patients was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Moreover, the presence of metastasis, either in general or specifically in the lung, was not associated with intrahost diversity among cancer patients. Cancer patients carried significantly higher numbers of minor variants compared to non-cancer counterparts. Further studies on SARS-CoV-2 diversity in especially vulnerable patients will shed light onto the understanding of the basis of COVID-19 different outcomes in humans.

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Genetic Consequences of Fence Confinement in a Population of White-Tailed Deer

Diversity ◽

10.3390/d13030126 ◽

2021 ◽

Vol 13 (3) ◽

pp. 126

Author(s):

Emily K. Latch ◽

Kenneth L. Gee ◽

Stephen L. Webb ◽

Rodney L. Honeycutt ◽

Randy W. DeYoung ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Wildlife Management ◽

Field Observations ◽

Adaptive Potential ◽

Population Isolation ◽

Potential Benefits ◽

Wildlife Populations ◽

Mtdna Diversity

Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 white-tailed deer confined within a 1184 ha fence to quantify changes in genetic diversity and inbreeding over the first 12 years of confinement. Genetic diversity was sustained over the course of the study, remaining comparable to unconfined white-tailed deer populations. Uneroded genetic diversity suggests that genetic drift is mitigated by a low level of gene flow, which supports field observations that the fence is not completely impermeable. In year 9 of the study, we observed an unexpected influx of mtDNA diversity and drop in inbreeding as measured by FIS. A male harvest restriction imposed that year increased male survival, and more diverse mating may have contributed to the inbreeding reduction and temporary genetic diversity boost we observed. These data add to our understanding of the long-term impacts of fences on wildlife, but also highlight the importance of continued monitoring of confined populations.

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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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