Haplotype diversity of preharvest sprouting QTLs in wheat

Genome ◽  
2007 ◽  
Vol 50 (2) ◽  
pp. 107-118 ◽  
Author(s):  
Francis C. Ogbonnaya ◽  
Muhammad Imtiaz ◽  
Ron M. DePauw
Keyword(s):  
Genetic Similarity ◽  
Genetic Relationships ◽  
Aegilops Tauschii ◽  
Haplotype Diversity ◽  
Preharvest Sprouting ◽  
Principal Coordinates Analysis ◽  
Factors Affecting ◽  
Type Allele ◽  
Principal Coordinates ◽  
Genomic Regions

Preharvest sprouting (PHS) is one of the most important factors affecting wheat production worldwide in environments characterized by rainfall and high humidity at harvest. In such environments, the incorporation of seed dormancy of a limited duration is required to minimize losses associated with PHS. A global collection of 28 PHS-resistant and -susceptible wheat germplasm was characterized with microsatellite markers flanking the genomic regions associated with PHS-resistance quantitative trait loci (QTLs), particularly on chromosomes 3D and 4A. The genetic diversity analysis revealed 380 alleles at 54 microsatellite loci, with an average of 7.0 alleles per locus, among the 28 wheat genotypes. Gower’s genetic similarity values among all possible pairs of genotypes varied from 0.44 to 0.97, indicating that there is considerable diversity in the PHS germplasm evaluated. Cluster and principal coordinates analysis of genetic similarity estimates differentiated the genotypes into groups, according to their source of PHS resistance. Three major SSR haplotypes were observed on chromosome 4AL, designated RL4137-type allele, Aus1408-type allele, and synthetic-hexaploid-type allele. The RL4137-type allele was prevalent in Canadian cultivars, mostly in cluster 6, followed by the Aus1408-type and its derivatives in clusters 4 and 5. The Syn36 and Syn37 alleles on chromosome 4AL were rare. On chromosome 3DL, the SSRs haplotypes derived from Syn36 and Syn37 were also rare, and proved unique to the Aegilops tauschii - derived synthetic hexaploids. They are therefore likely carrying resistance genes different from those previously reported. Based on genetic relationships, PHS resistance might be improved by selecting parental genotypes from different clusters.

scholarly journals Efficiency of RAPD and ISSR markers in assessing genetic diversity and relationships in black gram (Vigna mungo L. Hepper) vari

2010 ◽  
Vol 90 (4) ◽  
pp. 443-452 ◽  
Author(s):  
T. Karuppanapandian ◽  
H W Wang ◽  
T. Karuppudurai ◽  
J. Rajendhran ◽  
M. Kwon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Vigna Mungo ◽  
Polymorphic Band ◽  
Black Gram ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Rapd And Issr

The DNA fingerprinting methodologies, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR), were used to estimate genetic diversity and relationships among 20 black gram (Vigna mungo L. Hepper) varieties. Thirty selected RAPD primers amplified 255 bands, 168 of which were polymorphic (66.5%). On average, these primers produced 8.5 bands, 5.6 of which were polymorphic. Polymorphic band number varied from 2 (A-05) to 10 (OPA-02), with sizes ranging from 100 to 2550 bp. Twenty-four selected ISSR primers produced 238 amplified products, 184 of which were polymorphic (77.8%). On average, these primers generated 9.8 bands, with 7.7 polymorphic bands ranging in number from 4 (ISSR-13) to 11 (ISSR-03), and size from 100-2650 bp. Genetic relationships were estimated using similarity coefficient (Jaccard’s) values between different accession pairs; these varied from 30.7 to 85.0 for RAPD, and from 37.2 to 88.4 with ISSR. UPGMA analysis indicated that the varieties ranged in similarity from 0.50 to 1.00 (mean of 0.75) for RAPD, and from 0.47 to 1.00 (mean of 0.76) with ISSR. Cluster analysis of RAPD and ISSR results identified three clusters with significant bootstrap values, which revealed greater homology between the varieties. Principal coordinates analysis also supported this conclusion. Among the black gram varieties, WBU-108 and RBU-38 were highly divergent, whereas LBG-648 and LBG-623 were genetically similar. The markers generated by RAPD and ISSR assays can provide practical information for the management of genetic resources and these results will also provide useful information for the molecular classification and breeding of new black gram varieties.Key words: Black gram, cluster analysis, genetic diversity, ISSR, molecular markers, RAPD

Genetic relationships and variation among ecotypes of seashore paspalum (Paspalum vaginatum) determined by random amplified polymorphic DNA markers

Genome ◽  
1994 ◽  
Vol 37 (6) ◽  
pp. 1011-1017 ◽  
Author(s):  
Zhao-Wei Liu ◽  
Robert L. Jarret ◽  
Ronny R. Duncan ◽  
Stephen Kresovich
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Seashore Paspalum ◽  
Principal Coordinates ◽  
Paspalum Vaginatum ◽  
High Level

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic relationships and variation among ecotypes of the turfgrass seashore paspalum (Paspalum vaginatum Swartz). Vegetative tissues or seeds of 46 seashore paspalum ecotypes were obtained from various locations in the United States, Argentina, and South Africa. Leaf DNA extracts were screened for RAPD markers using 34 10-mer random primers. A total of 195 reproducible RAPD fragments were observed, with an average of six fragments per primer. One hundred and sixty-nine fragments (87% of the total observed) were polymorphic, among which 27 fragments (16%) were present in three or less ecotypes, indicating the occurrence of a high level of genetic variation among the examined accessions of this species. Cluster analysis (UPGMA) and principal coordinates analysis were performed on the RAPD data set. The results illustrate genetic relationships among the 46 ecotypes, and between ecotypes and their geographical origins. Ecotypes from southern Africa could be differentiated from the U.S. and most of the Argentinean ecotypes. With a few exceptions, ecotypes collected from Argentina, Hawaii, Florida, and Texas were separated into distinct clusters.Key words: RAPDs, polymerase chain reaction, genetic diversity, phenetic analysis.

Genetic diversity analysis using simple sequence repeat markers in soybean

2014 ◽  
Vol 12 (S1) ◽  
pp. S87-S90 ◽  
Author(s):  
Zhenbin Hu ◽  
Guizhen Kan ◽  
Guozheng Zhang ◽  
Dan Zhang ◽  
Derong Hao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Wild Soybean ◽  
Sequence Repeat ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Cultivated Soybean ◽  
Simple Sequence ◽  
Nei's Genetic Distance

To evaluate the genetic diversity (GD) of wild and cultivated soybeans and determine the genetic relationships between them, in this study, 127 wild soybean accessions and 219 cultivated soybean accessions were genotyped using 74 simple sequence repeat (SSR) markers. The results of the study revealed that the GD of the wild soybeans exceeded that of the cultivated soybeans. In all, 924 alleles were detected in the 346 soybean accessions using 74 SSRs, with an average of 12.49 alleles per locus. In the 219 cultivated soybean accessions, 687 alleles were detected, with an average of 9.28 alleles per locus; in the 127 wild soybean accessions, 835 alleles were detected, with an average of 11.28 alleles per locus. We identified 237 wild-soybean-specific alleles and 89 cultivated-soybean-specific alleles in the 346 soybean accessions, and these alleles accounted for 35.28% of all the alleles in the sample. Principal coordinates analysis and phylogenetic analysis based on Nei's genetic distance indicated that all the accessions could be classified into two major clusters, corresponding to wild and cultivated soybeans. These results will increase our understanding of the genetic differences and relationships between wild and cultivated soybeans and provide information to develop future breeding strategies to improve soybean yield.

scholarly journals Population Structure Within the Hard Maple Species Complex

2021 ◽  
Author(s):  
Whitney April Jackson ◽  
Joshua A. Honig ◽  
Peter E Smouse ◽  
Jason Grabosky
Keyword(s):  
Acer Saccharum ◽  
Species Complex ◽  
Sugar Maple ◽  
Genetic Relationships ◽  
Ecological Niches ◽  
Principal Coordinates Analysis ◽  
Sustainable Solutions ◽  
Principal Coordinates ◽  
Nursery Production ◽  
Ssr Loci

Sugar maple (Acer saccharum Marsh) is the most economically important member of the Hard Maple species complex, a group of related species that occupy a range between Canada and Mexico and adapted to distinct ecological niches. Sugar maple has been identified as vulnerable to rapid climate change, and sustainable solutions are needed to support its role in the production of maple sugar, as well as timber and nursery production in the northeastern US. Genetic relationships between sugar maple and its allies are largely unknown. In the current study, genetic relationships of 278 individuals from six hard maple species were assessed using 17multi-allelic microsatellite (SSR) loci. Genetic variance was partitioned into separate components for variation within and among populations, within and among species. Most of the divergence among populations (FPT = 0.263) reflected inter-specific divergence (FST = 0.169), but provenances within species also differed at non-trivial scales (FPS = 0.113). Estimation and testing of paired inter-provenance divergence showed that all population pairs were statistically divergent. Principal Coordinates Analysis (PCoA) indicated that the pattern of radiation observed among these taxa is broadly compatible with geography.

scholarly journals Genetic diversity and relationships of Chinese donkeys using microsatellite markers

2019 ◽  
Vol 62 (1) ◽  
pp. 181-187 ◽  
Author(s):  
Lulan Zeng ◽  
Ruihua Dang ◽  
Hong Dong ◽  
Fangyu Li ◽  
Hong Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Mean Value ◽  
Principal Coordinates Analysis ◽  
Expected Heterozygosity ◽  
Principal Coordinates ◽  
Baseline Information ◽  
Grouping Pattern ◽  
The Mean

Abstract. Donkeys are one important livestock in China because of their nourishment and medical values. To investigate the genetic diversity and phylogenetic relationships of Chinese donkey breeds, a panel of 25 fluorescently labeled microsatellite markers was applied to genotype 504 animals from 12 Chinese donkey breeds. A total of 226 alleles were detected, and the expected heterozygosity ranged from 0.6315 (Guanzhong) to 0.6999 (Jiami). The mean value of the polymorphism information content, observed number of alleles, and expected number of alleles for all the tested Chinese donkeys were 0.6600, 6.890, and 3.700, respectively, suggesting that Chinese indigenous donkeys have relatively abundant genetic diversity. Although there were abundant genetic variations found, the genetic differentiation between the Chinese donkey breeds was relatively low, which displayed only 5.99 % of the total genetic variance among different breeds. The principal coordinates analysis clearly splits 12 donkey breeds into two major groups. The first group included Xiji, Xinjiang, Liangzhou, Kulun, and Guanzhong donkey breeds. In the other group, Gunsha, Dezhou, Biyang, Taihang, Jiami, Qingyang, and Qinghai donkeys were clustered together. This grouping pattern was further supported by structure analysis and neighbor-joining tree analysis. Furthermore, genetic relationships between different donkey breeds identified in this study were corresponded to their geographic distribution and breeding history. Our results provide comprehensive and precise baseline information for further research on preservation and utilization of Chinese domestic donkeys.

ХАРАКТЕРИСТИКА АЛЛЕЛОФОНДА ХОЛМОГОРСКОЙ ПОРОДЫ КРУПНОГО РОГАТОГО СКОТА С ИСПОЛЬЗОВАНИЕМ STR-МАРКЕРОВ

2019 ◽  
pp. 3-7 ◽  
Author(s):  
V.V. VOLKOVA ◽  
O.S. ROMANENKOVA ◽  
T.E. DENISKOVA ◽  
A.I. MISHINA ◽  
O.V. KOSTYUNINA ◽  
...  
Keyword(s):  
Gene Pool ◽  
Genetic Relationships ◽  
Cattle Breed ◽  
Sample Collection ◽  
Principal Coordinates Analysis ◽  
Average Value ◽  
Holstein Breed ◽  
Principal Coordinates ◽  
Productive Traits ◽  
And Cluster Analysis

Для совершенствования продуктивных качеств холмогорской породы крупного рогатого скота, характеризующейся неприхотливостью и высокими адаптационными качествами, активно используется голштинизация. Данный процесс может привести к поглощению и утрате оригинального генофонда без своевременной оценки генетического состояния породы по ДНКмаркерам. Целью нашей работы стала генетическая характеристика аллелофонда популяций холмогорской породы с помощью STRмаркеров. Исследования проведены на 289 животных, включая генофондные пробы (СТКАМ, n68 и СТКОМИ, n24), Северный (ХОЛМ, n19), Татарстанский (ТАТ, n53) и Печорский (ПЕЧ, n125) типы. В качестве группы сравнения были использованы STRпрофили скота голштинской породы (ГОЛШ). Количество информативных аллелей варьировало от 4,36 в СТКОМИ до 4,91 в ХОЛМ и ПЕЧ и в среднем по холмогорской породе составило 4,67 по сравнению с 4,55 в голштинской. Эффективное число аллелей в холмогорской породе несколько превосходило значение данного показателя у голштинов (3,87 и 3,81 аллеля, соответственно). В популяциях крупного рогатого скота холмогорской породы был отмечен незначительный избыток гетерозигот. Минимальное значение FST (0,016) было зафиксировано между группами ТАТ и СТКАМ, в то время как максимальное наблюдалось между популяциями ПЕЧ и ГОЛШ (FST 0,041). Анализ главных координат (PCoA), структура дендрограммы и кластерный анализ выявили генетическую схожесть ПЕЧ и СТКОМИ, а также близкие генетические связи ТАТ и ГОЛШ.Кроме того, животные группы ПЕЧ характеризовались наличием генетического материала, который не встречался в других популяциях холмогорского скота. Полученные результаты свидетельствуют, что наряду со значительным генетическим влиянием голштинского скота исконный генофонд холмогорского скота не утрачен, что является важным фактором для разработки эффективных программ по сохранению данной породы.The crossing with the Holstein bulls is widely used to improve the productive traits of the Kholmogory cattle breed, characterized by unpretentiousness and high adaptive qualities. This process might result in a loss of the original gene pool of the Kholmogory cattle breed without assessment by DNA markers. In this regard, our aim was to perform genetic assessment of the allele pool of the populations of the Kholmogory cattle breed using STR markers. Sample collection included 289 heads of the Kholmogory cattle, including Old Kamchatka (STKAM, n68) and Old Komi groups (STKOMI, n24), Northern (KHOLM, n19), Tatar (TAT, n53) and Pechora (PECH, n125) types. The STR profiles of the animals from the Holstein breed (GOLSH) were used as a comparison group. The number of informative alleles varied from 4.36 in STKOMI to 4.91 in KHOLM and PECH with the average value for the Kholmogory breed in 4.67 in comparison with 4.55 in the Holstein breed. The effective number of alleles in the Kholmogory breed slightly exceeded the value of this indicator in the Holstein breed (3.87 and 3.81 alleles, respectively). All populations of the Kholmogory breed were characterized by a slight excess of heterozygotes. The minimum value of FST (0.016) was recorded between the TAT and CTKAM groups, while the maximum was observed between the populations of PECH and GOLSH (FST 0.041). The Principal Coordinates Analysis (PCoA), the structure of the dendrogram and cluster analysis revealed the genetic similarities between PECH and STKOMI, as well as close genetic relationships between TAT and GOLSH. In addition, the animals of the PECH group were characterized by the presence of the genetic background that was absent in other populations of the Kholmogory cattle. Thus, the results indicate that, along with the significant genetic influence of the Holstein cattle, the original gene pool of the Kholmogory cattle breed has not been lost, which is an important factor for the development of effective conservation programs for this breed.

scholarly journals Genetic Diversity of Remaining Populations of Mangaba (Hancornia speciosa Gomes) in Restingas of Brazil

2017 ◽  
Vol 9 (2) ◽  
pp. 46 ◽  
Author(s):  
Ana Veruska Cruz da Silva ◽  
Julie Anne Espíndola Amorim ◽  
Marília Freitas de Vasconcelos Melo ◽  
Ana Da Silva Ledo ◽  
Allivia Rouse Carregosa Rabbani
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Shannon Index ◽  
Conservation Strategies ◽  
Principal Coordinates Analysis ◽  
Fruit Species ◽  
Principal Coordinates ◽  
Hancornia Speciosa ◽  
Brazilian Northeast

Mangaba (Hancornia speciosa Gomes) is a fruit species that is native to Brazil, and has social, economic and cultural importance. Knowledge of the genetic relationships between the remaining populations is essential in order to promote conservation strategies for these genetic resources. In the present study, it was evaluated the genetic diversity of 35 individuals from three remaining restingas areas in the states of Ceará (Iguape and Cascavel) and Pernambuco (Tamandaré), located in the Brazilian Northeast. Nine ISSR primers were used to determine the genetic variability. Sixty-one fully polymorphic fragments (100%) were generated. The largest (10) and smallest (5) number of fragments were obtained with the primers HB14 and HB12, respectively. The Shannon index (I = 0.40), the genetic diversity (H = 0.30), and the percentage of polymorphic loci (%P = 73.77%) were also estimated. Both the methods of UPGMA and the Principal Coordinates Analysis (PCoA) clustered individuals according to their place of origin. Genetic divergence was greater within population (64%) than between them (36%). This may indicate a strong genetic structure, i.e., the gene flow rate between populations is low, favoring inbreeding. ISSR markers were efficient for the analysis of genetic diversity, for the identification of clusters, and for the estimation of the genetic distance between and within populations.

scholarly journals The Genetic Diversity and Structure of the European Turtle Dove Streptopelia turtur

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1283
Author(s):  
Petras Prakas ◽  
Dalius Butkauskas ◽  
Saulius Švažas ◽  
Antonio Bea ◽  
Vadym Yanenko ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
Haplotype Diversity ◽  
Long Distance ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
Palearctic Species ◽  
D Loop ◽  
Turtle Dove ◽  
Streptopelia Turtur

The European Turtle Dove, Streptopelia turtur, a long-distance migrant wintering in Africa, is a widespread Palearctic species. This species is classified as vulnerable and is undergoing a long-term demographic decline. The results of the previous study (based on mitochondrial (mtDNA) cytochrome-b (cytb) sequences of birds from Western and Southern Europe) indicated that the species was not genetically structured. We analysed the mtDNA cytb and D-loop of 258 birds collected from Morocco, Spain, and Ukraine. High genetic variability, expressed by haplotype diversity and nucleotide diversity, was revealed in both cytb (Hd = 0.905 ± 0.009, π = 0.00628 ± 0.00014) and the D-loop (Hd = 0.937 ± 0.009, π = 0.01502 ± 0.00034). SAMOVA and principal coordinates analysis revealed the birds belonged to two genetically distinct groups. One group included birds collected in Spain, while birds sampled in Morocco and Ukraine formed another group. Furthermore, significant genetic differentiation was identified between Turtle Doves from Morocco and Ukraine, and certain Spanish samples. The present results indicate that specific management and conservation plans relevant for the species in various regions should be applied. However, further nuclear DNA research and new studies (particularly in Eastern Europe) are necessary for the decisive results on genetic structure of this species.

AFLP analysis of genetic relationships in the genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae)

Genome ◽  
2007 ◽  
Vol 50 (1) ◽  
pp. 90-105 ◽  
Author(s):  
Martina Rex ◽  
Kerstin Patzolt ◽  
Katharina Schulte ◽  
Georg Zizka ◽  
Roberto Vásquez ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Molecular Data ◽  
Aflp Analysis ◽  
Long Distance ◽  
Aflp Data ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Centre Of Diversity ◽  
Branch Lengths ◽  
Species Groups

The neotropical genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae) comprises about 30 species, with a centre of diversity in semiarid to humid habitats of the Andean slopes and valleys of Bolivia. Morphologic differentiation of species is difficult because of a paucity of diagnostic characters, and little is known about the infrageneric phylogeny. Here, we present the results of an amplified fragment length polymorphism (AFLP) analysis of 77 Fosterella specimens, covering 18 recognized species and 9 as-yet undescribed morphospecies. Eight primer combinations produced 310 bands, which were scored as presence/absence characters. Neighbour-joining tree reconstruction revealed 12 clusters (A–L) with various levels of support. Well-supported species groups were also recovered by a principal coordinates analysis. With few exceptions, morphologically defined species boundaries were confirmed by the molecular data. Phylogenetic relationships between species groups remained ambiguous, however, because of short internal branch lengths. The AFLP data were complemented by a survey of the leaf anatomy of 19 Fosterella species. Species concepts and assemblages are discussed in the context of molecular, morphologic, anatomic, ecologic, and biogeographic data. The data suggest that accidental long-distance dispersal and founder events have been important for Fosterella speciation.

scholarly journals Molecular characterization of sesame germplasms of West Bengal, India using RAPD markers

2019 ◽  
Vol 63 (1) ◽  
pp. 15-24
Author(s):  
Soumen Saha ◽  
Tarak Nath Dhar ◽  
Parthadeb Ghosh ◽  
Tulsi Dey
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
West Bengal ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Similarity Coefficients ◽  
Principal Coordinates Analysis ◽  
High Genetic Diversity ◽  
Principal Coordinates

The aim of this research was to assess the genetic diversity of sesame (Sesamum indicum L.) and also to reveal the genetic relationships using the Random Amplified Polymorphic DNA (RAPD) markers. Fifteen sesame germplasms were collected from seven districts or four zones of West Bengal, India. A high genetic diversity was revealed by ten RAPD primers within and among the fifteen germplasms. The value of Jaccard’s similarity coefficients among and within the fifteen germplasms ranged from 0.287 to 0.725 which indicated high degree of genetic variability. Cluster analysis using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) grouped all the germplasms into three main clusters. Analysis of various genetic diversity indices strongly indicated high level of genetic diversity among the populations of four different regions. UPGMA analysis of four populations resulted into two groups and the results of Principal Coordinates Analysis (PCoA) depicted a clear distinction among the germplasms.

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