Genetic diversity analysis of Rhanterium eppaposum Oliv. by ISSRs reveals a weak population structure

Salameen, Fadila Al; Habibi, Nazima; Amad, Sami Al; Kumar, Vinod; Dashti, Jamal; Talebi, Lina; Doaij, Bashayer Al

doi:10.1016/j.cpb.2020.100138

Cited by 16 publications

(21 citation statements)

References 29 publications

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“…The results generated in this study confi rm the importance of molecular markers for the proposed objective, and this study is in agreement with other studies reported in the literature (Jiang et al, 2019;Al Salameen et al, 2020;Xiang et al, 2020;Zacarías-Correa et al, 2020). The results also reinforce the importance of application of this technique in studies of other native tree species that still lack greater investigation in the scientifi c community and are exposed to extinction.…”

Section: Hierarchicalsupporting

confidence: 91%

“…In addition, they do not require previous knowledge of target sequences (Ng and Tan, 2015;Grover and Sharma, 2016). Consequently, ISSR is an eff ective tool for a variety of purposes, including identifi cation of germplasm and evaluation of genetic diversity (Coutinho et al, 2014;Kumar and Agrawal, 2017;Cid-Contreras et al, 2019;Al Salameen et al, 2020;Xiang et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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GENETIC DIVERSITY IN AMBURANA (Amburana cearensis) ACCESSIONS: HIERARCHICAL AND OPTIMIZATION METHODS

et al. 2021

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The evaluation of accessions in a germplasm bank is essential for determining the potential parents in conservation programs, especially for native trees. This study aimed to determine the genetic diversity among 68 Amburana cearensis genotypes from different locations in the state of Pernambuco, Brazil. Their genetic patterns were evaluated by Inter Simple Sequence Repeat (ISSR) molecular markers and genetic divergence was evaluated through multivariate analyses using different clustering methods. The optimization method used (Tocher) was in agreement with all the hierarchical models used, in which clustering of the genotypes occurred similarly, specifically for the accession BB116, which is an important genetic material to be preserved and studied. Among the various hierarchical methods applied, the Average Linkage method exhibited higher discrimination power, allowing identification of a larger number of divergent groups, thus implying wide genetic diversity among A. cearensis accessions.

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Section: Hierarchicalsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

GENETIC DIVERSITY IN AMBURANA (Amburana cearensis) ACCESSIONS: HIERARCHICAL AND OPTIMIZATION METHODS

et al. 2021

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“…The phylogenetic tree from the GBS data formed three distinctive clusters. The high diversity of plant populations may be due to the evolutionary history, genetic drift, and geographic range of the species and their characteristics (Al Salameen et al, 2020). The genotypes representing the grain N and stalk N were randomly distributed over the phylogenetic tree.…”

Section: Population Structure and Diversity Studiesmentioning

confidence: 99%

Nitrogen Use Efficiency in Sorghum: Exploring Native Variability for Traits Under Variable N-Regimes

et al. 2021

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Exploring the natural genetic variability and its exploitation for improved Nitrogen Use Efficiency (NUE) in sorghum is one of the primary goals in the modern crop improvement programs. The integrated strategies include high-throughput phenotyping, next generation sequencing (NGS)-based genotyping technologies, and a priori selected candidate gene studies that help understand the detailed physiological and molecular mechanisms underpinning this complex trait. A set of sixty diverse sorghum genotypes was evaluated for different vegetative, reproductive, and yield traits related to NUE in the field (under three N regimes) for two seasons. Significant variations for different yield and related traits under 0 and 50% N confirmed the availability of native genetic variability in sorghum under low N regimes. Sorghum genotypes with distinct genetic background had interestingly similar NUE associated traits. The Genotyping-By-Sequencing based SNPs (>89 K) were used to study the population structure, and phylogenetic groupings identified three distinct groups. The information of grain N and stalk N content of the individuals covered on the phylogenetic groups indicated randomness in the distribution for adaptation under variable N regimes. This study identified promising sorghum genotypes with consistent performance under varying environments, with buffer capacity for yield under low N conditions. We also report better performing genotypes for varied production use—grain, stover, and dual-purpose sorghum having differential adaptation response to NUE traits. Expression profiling of NUE associated genes in shoot and root tissues of contrasting lines (PVK801 and HDW703) grown in varying N conditions revealed interesting outcomes. Root tissues of contrasting lines exhibited differential expression profiles for transporter genes [ammonium transporter (SbAMT), nitrate transporters (SbNRT)]; primary assimilatory (glutamine synthetase (SbGS), glutamate synthase (SbGOGAT[NADH], SbGOGAT[Fd]), assimilatory genes [nitrite reductase (SbNiR[NADH]3)]; and amino acid biosynthesis associated gene [glutamate dehydrogenase (SbGDH)]. Identification and expression profiling of contrasting sorghum genotypes in varying N dosages will provide new information to understand the response of NUE genes toward adaptation to the differential N regimes in sorghum. High NUE genotypes identified from this study could be potential candidates for in-depth molecular analysis and contribute toward the development of N efficient sorghum cultivars.

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“…Although LEA and DAPC using BIC suggested a single cluster to be optimal, DAPC using AIC suggested two optimal clusters: one containing the Walla Walla Basin and the other with the remaining populations from Palouse and Kashmir Valley. This weak clustering indicates a weak population structure and that the populations have recently diverged, that ongoing migration promotes gene flow among the populations, or both ( Loveless and Hamrick 1984 ; Edwards et al 2020 ; Al Salameen et al 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure of a global invader Mayweed chamomile (Anthemis cotula): management implications

et al. 2021

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Mayweed chamomile (Anthemis cotula L.) is a globally invasive, troublesome annual weed but knowledge of its genetic diversity, population structure in invaded regions, and invasion patterns remains unstudied. Therefore, germplasm from 19 A. cotula populations (sites) from three geographically distinct invaded regions: the Walla Walla Basin (located in southern Washington) and the Palouse (located in both northern Idaho and eastern Washington), Pacific Northwest, USA and Kashmir Valley, India were grown in the greenhouse for DNA extraction and sequencing. A total of 18,829 SNPs were called and filtered for each of 89 samples. Pairwise-FST , Nei’s genetic distance, heterozygosity, Wright’s inbreeding coefficient (F), and self-fertilization rates were estimated for populations within and among the three regions with a total of 19 populations comprised of 89 individuals. Overall measurements of genetic variation were low but significant among regions, populations, and individuals. Despite the weak genetic structure, two main genetic clusters were evident, one comprised of populations from Palouse and Kashmir Valley, the other comprised of populations from the Walla Walla Basin. Significant selfing was observed in populations from the Walla Walla Basin and Palouse but not from Kashmir Valley, indicating that Mayweed chamomile in the Pacific Northwest USA could persist with low pollinator or pollen donor densities. Although FST values between the regions indicate Palouse populations are more closely related to Kashmir Valley than to Walla Walla Basin populations. Based on Migrate-n analysis, panmixis was the most likely model, suggesting an unrestricted gene flow among all three regions. Our study indicated that Kashmir Valley populations either originated from or shared the origin with the Palouse populations, suggesting human-mediated migration of A. cotula between regions.

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Genetic diversity analysis of Rhanterium eppaposum Oliv. by ISSRs reveals a weak population structure

Cited by 16 publications

References 29 publications

GENETIC DIVERSITY IN AMBURANA (Amburana cearensis) ACCESSIONS: HIERARCHICAL AND OPTIMIZATION METHODS

GENETIC DIVERSITY IN AMBURANA (Amburana cearensis) ACCESSIONS: HIERARCHICAL AND OPTIMIZATION METHODS

Nitrogen Use Efficiency in Sorghum: Exploring Native Variability for Traits Under Variable N-Regimes

Genetic diversity and population structure of a global invader Mayweed chamomile (Anthemis cotula): management implications

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