scholarly journals Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Xuan Wang ◽  
Fei Shen ◽  
Yuan Gao ◽  
Kun Wang ◽  
Ruiting Chen ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Indel Markers ◽  
Genome Wide ◽  
Genetic Patterns ◽  
Golden Delicious ◽  
Unique Identity ◽  
High Level ◽  
Cultivation History

Abstract Background Apple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, whole-genome structural variants identified between M. domestica cultivars ‘Jonathan’ and ‘Golden Delicious’ were used. Results A total of 25,924 insertions and deletions (InDels) were obtained, from which 102 InDel markers were developed. Using the InDel markers, we found that 942 (75.3%) of the 1251 Malus accessions from 35 species exhibited a unique identity signature due to their distinct genotype combinations. The 102 InDel markers could distinguish 16.7–71.4% of the 331 bud sports derived from ‘Fuji’, ‘Red Delicious’, ‘Gala’, ‘Golden Delicious’, and other cultivars. Five distinct genetic patterns were found in 1002 diploid accessions based on 78 bi-allele InDel markers. Genetic structure analysis indicated that M. domestica showed higher genetic diversity than the other species. Malus underwent a relatively high level of wild-to-crop or crop-to-wild gene flow. M. sieversii was closely related to both M. domestica and cultivated Chinese cultivars. Conclusions The identity signatures of Malus accessions can be used to determine distinctness, uniformity, and stability. The results of this study may also provide better insight into the genetic relationships among Malus species.

Genome-wide Development of Insertion-deletion (InDel) Markers Database for Cannabis and its uses for Genetic Structure Analysis of Chinese Germplasm and Identification of Sex-linked Marker

2021 ◽  
Author(s):  
Gen Pan ◽  
Zheng Li ◽  
Siqi Huang ◽  
Jie Tao ◽  
Yaliang Shi ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Cannabis Sativa ◽  
Economic Value ◽  
Germplasm Conservation ◽  
Polymorphism Analysis ◽  
Indel Markers ◽  
Genome Wide ◽  
A Genome ◽  
Indel Polymorphisms ◽  
Chinese Germplasm

Abstract Background: Cannabis sativa L., a dioecious plant, derived from China, demonstrates important medicinal properties and economic value worldwide. Cannabis properties were usually harnessed depending on the sex of the plant. To analyze the genetic structure of Chinese cannabis and identify sex-linked makers, the genome-wide insertion-deletion (InDel) markers were designed and used. Results: In this study, a genome-wide analysis of insertion–deletion (InDel) polymorphisms was performed based on the recent genome sequences. In total, 47558 InDels were detected between the two varieties, and the length of InDels ranged from 4 bp to 87 bp. The most common InDels were tetranucleotides, followed by pentanucleotides. Chromosome 5 had the highest number of InDels among the cannabis chromosomes, while chromosome 10 had the lowest number. Additionally, a total of 47558 InDel markers were designed, and 84 primers evenly distributed in the cannabis genome were chosen for polymorphism analysis. A total of 38 primers exhibited polymorphisms among three accessions, and of the polymorphism primers, 14 biallelic primers were further used to analyse the genetic structure. A total of 39 fragments were detected, and the PIC value ranged from 0.1209 to 0.6351. According to the Indel markers as well as the flowering time, the 115 Chinese germplasms were divided in two subgroups, which were mainly composed of cultivars from the most north and south regions, respectively. Additional, the marker “ I1-10” was found to amplify two bands (398bp and 251bp) in the male plants, while a 389bp bands in female plants. Using this marker, the feminized and dioecious varieties can also be distinguished.Conclusion: This study will facilitate the genetic improvement and germplasm conservation of cannabis in China, and the sex-linked InDel markers will provide accurate sex identification strategies for cannabis breeding and production.

Yersinia genome diversity disclosed by Yersinia pestis genome-wide DNA microarray

2007 ◽  
Vol 53 (11) ◽  
pp. 1211-1221 ◽  
Author(s):  
Xiaoyi Wang ◽  
Yanping Han ◽  
Yanjun Li ◽  
Zhaobiao Guo ◽  
Yajun Song ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Genetic Relationships ◽  
Opportunistic Pathogens ◽  
Pcr Screening ◽  
Genomic Plasticity ◽  
Yersinia Species ◽  
Genome Wide ◽  
Chromosomal Genes ◽  
Conserved Gene ◽  
High Level

The genus Yersinia includes 11 species, 3 of which ( Y. pestis , Y. pseudotuberculosis , and Y. enterocolitica ) are pathogenic for humans. The remaining 8 species ( Y. frederiksenii , Y. intermedia , Y. kristensenii , Y. bercovieri , Y. mollaretii , Y. rohdei , Y. ruckeri , and Y. aldovae ) are merely opportunistic pathogens found mostly in the environment. In this work, the genomic differences among Yersinia were determined using a Y. pestis-specific DNA microarray. The results revealed 292 chromosomal genes that were shared by all Yersinia species tested, constituting the conserved gene pool of the genus Yersinia. Hierarchical clustering analysis of the microarray data revealed the genetic relationships among all 11 species in this genus. The microarray analysis in conjunction with PCR screening greatly reduced the number of chromosomal genes (32) specific for Y. pestis to 16 genes and uncovered a high level of genomic plasticity within Y. pseudotuberculosis, indicating that its different serotypes have undergone an extensively parallel loss or acquisition of genetic content, which is likely to be important for its adaptation to changes in environmental niches.

scholarly journals Genome-wide development of insertion-deletion (InDel) markers for Cannabis and its uses in genetic structure analysis of Chinese germplasm and sex-linked marker identification

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gen Pan ◽  
Zheng Li ◽  
Siqi Huang ◽  
Jie Tao ◽  
Yaliang Shi ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Cannabis Sativa ◽  
Economic Value ◽  
Germplasm Conservation ◽  
Polymorphism Analysis ◽  
Indel Markers ◽  
Genome Wide ◽  
A Genome ◽  
Indel Polymorphisms ◽  
Chinese Germplasm

Abstract Background Cannabis sativa L., a dioecious plant derived from China, demonstrates important medicinal properties and economic value worldwide. Cannabis properties have been usually harnessed depending on the sex of the plant. To analyse the genetic structure of Chinese Cannabis and identify sex-linked makers, genome-wide insertion-deletion (InDel) markers were designed and used. Results In this study, a genome-wide analysis of insertion-deletion (InDel) polymorphisms was performed based on the recent genome sequences. In total, 47,558 InDels were detected between the two varieties, and the length of InDels ranged from 4 bp to 87 bp. The most common InDels were tetranucleotides, followed by pentanucleotides. Chromosome 5 exhibited the highest number of InDels among the Cannabis chromosomes, while chromosome 10 exhibited the lowest number. Additionally, 31,802 non-redundant InDel markers were designed, and 84 primers evenly distributed in the Cannabis genome were chosen for polymorphism analysis. A total of 38 primers exhibited polymorphisms among three accessions, and of the polymorphism primers, 14 biallelic primers were further used to analyse the genetic structure. A total of 39 fragments were detected, and the PIC value ranged from 0.1209 to 0.6351. According to the InDel markers and the flowering time, the 115 Chinese germplasms were divided into two subgroups, mainly composed of cultivars obtained from the northernmost and southernmost regions, respectively. Additional two markers, “Cs-I1–10” and “Cs-I1–15”, were found to amplify two bands (398 bp and 251 bp; 293 bp and 141 bp) in the male plants, while 389-bp or 293-bp bands were amplified in female plants. Using the two markers, the feminized and dioecious varieties could also be distinguished. Conclusion Based on the findings obtained herein, we believe that this study will facilitate the genetic improvement and germplasm conservation of Cannabis in China, and the sex-linked InDel markers will provide accurate sex identification strategies for Cannabis breeding and production.

Nematode population genetics

1998 ◽  
Vol 72 (4) ◽  
pp. 281-283 ◽  
Author(s):  
M.E. Viney
Keyword(s):  
Population Genetics ◽  
Genetic Structure ◽  
Population Genetic ◽  
Genetic Relationships ◽  
Parasitic Nematodes ◽  
Important Group ◽  
Nematode Parasites ◽  
Genetic Patterns ◽  
Patterns And Processes ◽  
Epidemiological Information

Population genetics seeks to understand the genetic relationships within and between populations of a species and the processes that generate these patterns. Little is known about the population genetics of parasitic nematodes. This is a notable gap in our knowledge since understanding the population genetic patterns and processes of parasitic nematodes has profound implications for our ability to fully understand this important group of pathogens. For example, it is only possible to begin to understand how a parasite population will respond to an imposed selection pressure (such as an anthelmintic drug, a vaccine, or resistant hosts) when the population genetic structure and patterns of gene flow of that population is known. Equally, the epidemiology of many nematode parasites is well known empirically and theoretically, yet this epidemiological information is of limited use without a good understanding of the genetic structure of those populations (Anderson & May, 1992).

scholarly journals Differentiation and genetic diversity of Phaseolus lunatus wild populations from Chiapas, Mexico, and their genetic relationships with MI and MII groups

2016 ◽  
Vol 94 (4) ◽  
pp. 712
Author(s):  
Pedro Jesús Ruiz-Gil ◽  
Gabriel Chepe-Cruz ◽  
Rubén Humberto Andueza-Noh ◽  
Matilde Margarita Ortiz-García ◽  
Jaime Martínez-Castillo
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Divergence ◽  
Genetic Relationships ◽  
Lima Bean ◽  
Phaseolus Lunatus ◽  
Gene Pools ◽  
Wild Populations ◽  
Isthmus Of Tehuantepec ◽  
High Level

<p><strong>Background</strong><em>. </em>Understanding the genetic structure of wild relatives of domesticated species is crucial for its conservation and to elucidate the sites of crop domestication. Lima bean is one of the five domesticated <em>Phaseolus</em> species and Mexico is one of its centers of domestication. Recent studies showed the existence of two wild gene pools (MI and MII) of this species in Mexico and suggested that their genetic divergence occurred in southeast Mexico.</p><p><strong>Question</strong><em>. </em>Did MI and MII groups diverged around the Isthmus of Tehuantepec, Mexico?</p><p><strong>Studied species</strong><em>. </em>Lima bean: Neotropical plant species, herbaceous, with an annual/short life cycle and with autogamous tendency.</p><p><strong>Study site and years of study</strong><em>. </em>Seven wild populations were collected in 2012 in the State of Chiapas, México, area underrepresented in previous studies.</p><p><strong>Methods</strong><em>. </em>Genetic diversity and grouping patterns of collected populations and their relationship to MI and MII groups were analyzed at eight microsatellite loci.</p><p><strong>Results</strong>. High genetic structure (<em>F</em><sub>ST</sub>: 0.42 to 0.96) and a high level of genetic diversity (<em>H</em><sub>E </sub>= 0.48) were found. The analyses, and presence of admixed populations in MI and MII, suggested that the genetic divergence of these groups is an ongoing process centered around the Isthmus of Tehuantepec.</p><p><strong>Conclusions</strong><em>. </em>Our results support the hypothesis that MI and MII groups diverged around the Isthmus of Tehuantepec; however, sampling should be increased both at population and genomic levels, to determine the precise organization of the genetic diversity of wild <em>P. lunatus</em> from Mexico.</p>

CONNECTION g.307 G > A SNP POLYMORPHISM OF THE ALPHA-FUKOZYLTRASFERAZA 1 GENE WITH ECONOMIC-USEFUL TRAITS IN THE LARGE WHITE PIG BREED

2017 ◽  
Vol 54 ◽  
pp. 134-140
Author(s):  
H. S. Rudoman ◽  
V. M. Balatsky ◽  
V. Y. Nor ◽  
V. O. Vovk
Keyword(s):  
Genetic Structure ◽  
Information Content ◽  
Analysis Of Variance ◽  
Farm Animals ◽  
Daily Weight Gain ◽  
Fixation Index ◽  
Its Sequencing ◽  
Large White ◽  
Stage Of Development ◽  
High Level

One of the top priorities at the present stage of development of pig breeding remains the development of a set of measures aimed at increasing the resistance animals to various diseases, especially – to colibacteriosis .One of the recent and effective approaches to prevent colibacillosis is using markers of selection; it involves pig genotyping by genome locuses. Chosen locuses are associated with animal sensitivity to the disease and selection of the results of genotyping of animals with increased resistance. Due to researches, one of such locuses is alpha-fukozyltrasferаza 1 gene (FUT1). Gene FUT1 is located in chromosome 6. As a result of its sequencing in the swine breeds of Large White and Swedish Landrace, single-nucleotide polymorphism (g.307 G > A SNP) has been detected. AA genotype determines the resistance of animals to colibacteriosis, while AG and GG genotypes are susceptible to this disease. According to the results of previous studies, the positive effect of allele A was determined not only on the resistance of pigs to colibacteriosis, but also on indicators of fattening and meat productivity and on reproductive performance. In Ukraine, the studies of polymorphism FUT1 g.307 G > A SNP were held fragmentedly and only on certain populations of Ukrainian Meat and Large White breed but without establishing its association with the indicators of productivity of pigs. The aim of our work was to study the genetic structure of Ukrainian Large White breeds, type 1 and the establishment of association. g. 307 G > A SNP FUT1 gene with pigs indicators of productivity. For research the 96 samples of hair were used. DNA isolation from samples with biomaterial were carried out using ion exchange resin Chelex-100. Genotyping was performed by PCR-RFLP by method of Jorgensen et al. (2006). Using DNA analysis of this breeds locus FUT1 was determined by genetic structure. Allele frequency of allele G (0,573) and allele A (0,427) was established The distribution of genotype frequencies was not statistically significantly different from the theoretically expected, calculated by the Hardy-Weinberg criterion. Thus, according to the locus of FUT1 g.307 G > A, the breeds investigated are in a state close to the genetic equilibrium. The negative value of the fixation index by the locus FUT1 g.307 G > A indicates an excess of heterozygotes in the population, and hence the lack of targeted selection for this marker. The valuation was performed by calculating the PIC (polymorphic information content) – information content of polymorphism marker. In the analyzed pig herd for this marker, the PIC has an average value (0,367), which indicates the high level of polymorphism of the given locus and is favorable for the possibility of conducting a search for links between individual genotypes and indicators of productivity. To establish the association g.307 G > A SNP FUT1 gene with indicators of animal productivity, a one-way analysis of variance of the experimental data was used. Based on the results of a one-way analysis of variance, a significant effect of the genotypes of the FUT1gene (g.1849 G > C) on the indicator of the average daily weight gain (р ≤ 0,001), the thickness of the bacon at the level of the VI-VII vertebrae (p ≤ 0.01), reaching live weight of 100 kg (р ≤ 0,001) and breeding index of fattening qualities (р ≤ 0,01) was found. The parameter of the influence of the genetic factor on the test feature was 28,54%, 10,4%, 33,4% and 8,8% respectively. According to the investigated indicators of productivity, animals with genotype AA, which determines resistance to colibacteriosis, dominated the animals with genotypes GG and AG. Based on the results of our research and pre-published data, the multiple effect of the g.307 G > A SNP FUT1 gene is observed, which is associated with the indicators of productivity, which again confirms the polygenicity of the quantitative trait loci of farm animals. Taking into account a high level of polymorphism of the investigated gene and reliable associations of genotypes with indicators of productivity found, it can be recommended to carry out breeding of pigs using genetic information of the g.307 G > A SNP gene FUT1.

scholarly journals Autosomal Microsatellite Investigation Reveals Multiple Genetic Components of the Highlanders from Thailand

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 383
Author(s):  
Aornpriya Mawan ◽  
Nonglak Prakhun ◽  
Kanha Muisuk ◽  
Suparat Srithawong ◽  
Metawee Srikummool ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Relationships ◽  
Forensic Investigation ◽  
Northern Thailand ◽  
Hill Tribe ◽  
Genetic Components ◽  
Large Populations ◽  
Population Interactions ◽  
Hill Tribes ◽  
The Hill

The hill tribes of northern Thailand comprise nine officially recognized groups: the Austroasiatic-speaking (AA) Khmu, Htin and Lawa; the Hmong-Mien-speaking (HM) IuMien and Hmong; and the Sino-Tibetan-speaking (ST) Akha, Karen, Lahu and Lisu. Except the Lawa, the rest of the hill tribes migrated into their present habitats only very recently. The Thai hill tribes were of much interest to research groups focusing on study of cultural and genetic variation because of their unique languages and cultures. So far, there have been several genetic studies of the Thai hill tribes. However, complete forensic microsatellite database of the Thai hill tribes is still lacking. To construct such database, we newly generated 654 genotypes of 15 microsatellites commonly used in forensic investigation that belong to all the nine hill tribes and also non-hill tribe highlanders from northern Thailand. We also combined 329 genotypes from previous studies of northern Thai populations bringing to a total of 983 genotypes, which were then subjected to genetic structure and population relationships analyses. Our overall results indicated homogenous genetic structure within the HM- and Tai-Kadai (TK)-speaking groups, large genetic divergence of the HM-speaking Hmong but not IuMien from the other Thai groups, and genetic heterogeneity within the ST- and AA-speaking groups, reflecting different population interactions and admixtures. In addition to establishing genetic relationships within and among these populations, our finding, which provides a more complete picture of the forensic microsatellite database of the multiple Thai highland dwellers, would not only serve to expand and strengthen forensic investigation in Thailand, but would also benefit its neighboring countries of Laos and Myanmar, from which many of the Thai hill tribes originated and where large populations of these ethnic groups still reside.

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

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