Molecular variability and genetic relationship and structure of Iranian Prunus rootstocks revealed by SSR and AFLP markers

Zeinalabedini, Mehrshad; Jalil, Dezhampour; Majidian, Parastoo; Khakzad, Motahareh; Zanjani, Bahram Maleki; Soleimani, Ali; Farsi, Maryam

doi:10.1016/j.scienta.2014.04.006

Cited by 13 publications

(8 citation statements)

References 35 publications

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“…Additionally, AMOVA analysis (Table 5) also indicated a low percentage of variation (4.24%) among populations. Similar results could be found in other trees [7,35].…”

Section: Discussionsupporting

confidence: 90%

SLAF-seq Uncovers the Genetic Diversity and Adaptation of Chinese Elm (Ulmus parvifolia) in Eastern China

Lyu

Dong

Huang

et al. 2020

Forests

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The Chinese elm is an important tree ecologically; however, little is known about its genetic diversity and adaptation mechanisms. In this study, a total of 107 individuals collected from seven natural populations in eastern China were investigated by specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) detected by SLAF-seq, genetic diversity and markers associated with climate variables were identified. All seven populations showed medium genetic diversity, with PIC values ranging from 0.2632 to 0.2761. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Environmental association analyses with three climate variables (annual rainfall, annual average temperature, and altitude) resulted in, altogether, 43 and 30 putative adaptive loci by Bayenv2 and LFMM, respectively. Five adaptive genes were annotated, which were related to the functions of glycosylation, peroxisome synthesis, nucleic acid metabolism, energy metabolism, and signaling. This study was the first on the genetic diversity and local adaptation in Chinese elms, and the results will be helpful in future work on molecular breeding.

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“…Additionally, AMOVA analysis (Table 5) also indicated a low percentage of variation (4.24%) among populations. Similar results could be found in other trees [7,35].…”

Section: Discussionsupporting

confidence: 90%

SLAF-seq Uncovers the Genetic Diversity and Adaptation of Chinese Elm (Ulmus parvifolia) in Eastern China

Lyu

Dong

Huang

et al. 2020

Forests

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“…Most of such phylogenetic trees are unable to display some parameters, such as horizontal gene transfer, hybridization, and recombination [29]. As a result, phylogenetic networks (NNet) analysis was used to explain visualized conflicting signals in the data sets, whether they arise from sampling error or genuine recombination [40,41]. The NNet analysis categorized the cultivars into two groups, which again show the territoriality (Figure 1B).…”

Section: Discussionmentioning

confidence: 99%

ISSR Analysis of Genetic Diversity and Structure of Plum Varieties Cultivated in Southern China

Chen

Yeh

et al. 2018

Biology

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Plums (Prunus spp.) are important deciduous fruit crops in the world. China is a major producer of P. salicina Lindl., but the genetic relationship of Chinese plums in key production regions remain unclear. In this study, 14 University of British Columbia (UBC) inter simple sequence repeats (ISSR) primers were used to analyze 33 plum varieties cultivated in Fujian Province to determine their genetic diversity and population structure. A total of 146 bands were generated, of which 130 were polymorphic. Mean percentage of polymorphic bands was 89.04%, Shannon’s information index value was 0.38, and the Nei’s genetic index value was 0.24. Using unrooted trees (Neighbor-Joining method), 33 varieties were classified into four groups. Split graph separated them into two major groups, each with two subgroups. The two phylogenetic trees indicate that environmental or natural selection pressure is an important factor influencing their genetic relationship. Analysis of population structure revealed that they have frequent genetic exchanges among closed subpopulations; thus, genetic variation mainly occurs within the population. Additionally, based on the phylogenetic analysis and unique morphological characteristics of fruits, we propose that the Chinese landrace Nai could contribute significantly to development of the famous variety Wickson.

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“…The rapid development of technology and the accompanying needs, the facilities of the laboratories where the applications will occur, the biological properties of the species and the abundance of markers in the genome have contributed to the development of DNA markers [5]. Restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA markers (RAPD), amplified fragment length polymorphism (AFLP), sequence labeled sequences (STS), microsatellites (SSR), cleaved polymorphic sequence (CAPS), single strand such as complementary polymorphism (SSCP), amplicon length polymorphism (ALP), interspecific sequence repeat polymorphism (ISSR), expressed sequence tags (EST) and single nucleotide polymorphism (SNP) [1,[6][7][8][9][10][11].…”

Section: Molecular Marker Analysismentioning

confidence: 99%

“…Molecular marker techniques have some advantages and disadvantages as compared to each other, but their reasons for preference vary according to the purpose of the study and the technical possibilities of the laboratory in which the study will be conducted. SSR and SNP markers are frequently preferred because of the high level of polymorphism nowadays [11,12].…”

Section: Molecular Marker Analysismentioning

confidence: 99%

Introductory Chapter: New Age Molecular Techniques in Plant Science

Celik¹

2018

New Visions in Plant Science

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Molecular variability and genetic relationship and structure of Iranian Prunus rootstocks revealed by SSR and AFLP markers

Cited by 13 publications

References 35 publications

SLAF-seq Uncovers the Genetic Diversity and Adaptation of Chinese Elm (Ulmus parvifolia) in Eastern China

SLAF-seq Uncovers the Genetic Diversity and Adaptation of Chinese Elm (Ulmus parvifolia) in Eastern China

ISSR Analysis of Genetic Diversity and Structure of Plum Varieties Cultivated in Southern China

Introductory Chapter: New Age Molecular Techniques in Plant Science

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