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

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.

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Haplotype diversity of preharvest sprouting QTLs in wheat

Genome ◽

10.1139/g06-142 ◽

2007 ◽

Vol 50 (2) ◽

pp. 107-118 ◽

Cited By ~ 27

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.

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Qualitative and quantitative variation in the macrobenthic fauna of the Original Lake and new lake areas of Great Lake and Arthurs Lake, Tasmania

Marine and Freshwater Research ◽

10.1071/mf9830787 ◽

1983 ◽

Vol 34 (5) ◽

pp. 787 ◽

Cited By ~ 5

Author(s):

W Fulton

Keyword(s):

Great Lake ◽

Quantitative Data ◽

Benthic Fauna ◽

Principal Coordinates Analysis ◽

Qualitative And Quantitative ◽

Principal Coordinates ◽

Annual Biomass ◽

Species Groups ◽

The Mean ◽

Flooded Areas

Faunal variation between sample sites in Great Lake and Arthurs Lake, using both qualitative and quantitative data, was analysed. Cluster analysis and principal coordinates analysis showed that the fauna of the original lake areas of both lakes is distinct from the fauna of the newly flooded areas. Closer relationships exist between the faunas of the old level of the two lakes than between the faunas of the old and new levels within either lake. The distinction is not attributable to depth but may be influenced by substrate differences. The effects of abnormal fluctuations in water level on benthic fauna are discussed. Biomass variation between the sample sites was examined in relation to component species groups. The sites at the old level were dominated by oligochaetes whereas chironomids contributed most to the sites at the new level. Consistent seasonal peaks were evident in the biomass at sites at the new level but not at sites at the old. The mean annual biomass levels (wet wt) for Great Lake (13.9 g m-2) and Arthurs Lake (35.9 g m-2) are compared with recorded values for other Australian and overseas lakes. Biomass levels of Australian lakes in general are also discussed.

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

Canadian Journal of Plant Science ◽

10.4141/cjps10014 ◽

2010 ◽

Vol 90 (4) ◽

pp. 443-452 ◽

Cited By ~ 2

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

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Understanding population differentiation using geographical, morphological and genetic characterization in Erodium cicunium

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.80.4.12 ◽

2020 ◽

Vol 80 (04) ◽

Author(s):

Xingxing Si ◽

Lei GAO ◽

Yuwei Song ◽

Majid Khayatnezhad ◽

Amir Abbas Minaeifar

Keyword(s):

Genetic Difference ◽

Morphological Characters ◽

Molecular Data ◽

Population Diversity ◽

Start Codon ◽

Principal Coordinates Analysis ◽

Forage Plants ◽

Principal Coordinates ◽

Geographical Populations ◽

Study Population

Erodium cicunium (Geraniaceae) species are distributed in different habitats of Iran. Some species are of medicinal importance while some are well known weeds and used as forage plants. An investigation was carried out to evaluate 124 randomly collected plants of E. cicunium from 15 geographical populations in 5 provinces to study population structure and for morphological and molecular characters. Start Codon Targeted (SCoT) markers were used to analyse molecular diversity. Analysis of molecular variance (AMOVA) revealed significant genetic difference among the studied populations and also revealed that 60% of total genetic variability was due to within population diversity, while 40% genetic differentiation was recorded among populations. Principal Coordinates Analysis (PCoA) of populations based on morphological characters was not in agreement with Metric Multidimensional Scaling (MDS) plot of molecular data.

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

Genome ◽

10.1139/g94-143 ◽

1994 ◽

Vol 37 (6) ◽

pp. 1011-1017 ◽

Cited By ~ 37

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.

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Genetic diversity analysis using simple sequence repeat markers in soybean

Plant Genetic Resources ◽

10.1017/s1479262114000331 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S87-S90 ◽

Cited By ~ 2

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.

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Population Structure Within the Hard Maple Species Complex

Canadian Journal of Forest Research ◽

10.1139/cjfr-2020-0411 ◽

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.

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Genetic diversity and relationships of Chinese donkeys using microsatellite markers

Archives Animal Breeding ◽

10.5194/aab-62-181-2019 ◽

2019 ◽

Vol 62 (1) ◽

pp. 181-187 ◽

Cited By ~ 2

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.

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

Molochnoe i miasnoe skotovodstvo ◽

10.33943/mms.2019.7.42224 ◽

2019 ◽

pp. 3-7 ◽

Cited By ~ 3

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.

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Molecular and phenotypic diversity among chickpea (Cicer arietinum) genotypes as a function of drought tolerance

Crop and Pasture Science ◽

10.1071/cp17284 ◽

2018 ◽

Vol 69 (2) ◽

pp. 142 ◽

Cited By ~ 4

Author(s):

Supriya Sachdeva ◽

C. Bharadwaj ◽

Vinay Sharma ◽

B. S. Patil ◽

K. R. Soren ◽

...

Keyword(s):

Drought Tolerance ◽

Phenotypic Diversity ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Similarity Coefficients ◽

Principal Coordinates Analysis ◽

Breeding Programs ◽

Average Value ◽

Principal Coordinates

Diversity as a function of drought tolerance may be identified by morphological characters, and molecular tools used to find the most divergent genotypes for breeding programs for drought tolerance in future. The narrow genetic base of chickpea can be circumvented by using diverse lines in breeding programs. Forty chickpea genotypes were studied for their morphological and molecular diversity with an objective of identifying the most diverse drought-tolerant lines. In total, 90 alleles were detected with 3.6 alleles per locus. Polymorphism information content (PIC) values ranged from 0.155 to 0.782 with an average value of 0.4374 per locus. The size of amplified products ranged from 160 bp to 390 bp. Primer TA136 with eight alleles showed the highest PIC value of 0.7825, indicating its ability to differentiate the genotypes at molecular level. DARwin neighbour-joining tree analysis based on dissimilarity estimates was done for the molecular data and sequential agglomerative hierarchical non-overlapping (SAHN) grouping for the morphological data. It could clearly discriminate the tolerance and the sensitivity of genotypes. Two-dimensional principal coordinates analysis (PCoA) plot indicated good diversity for drought tolerance. The genetic similarity coefficients ranged from 0.115 (genotypes BGD72 to ICCV 5308) to 0.828 (genotypes ICCV 10316 to ICCV 92337).

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