Genetic diversity of Indian jujube cultivars using SCoT, ISSR, and rDNA markers

Singh, Sunil Kumar; Chhajer, Sidhika; Pathak, Rakesh; Bhatt, R. K.; Kalia, Rajwant K.

doi:10.1007/s11295-016-1092-x

Cited by 25 publications

(9 citation statements)

References 40 publications

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“…At the species level, the genetic diversity of M . lutarioriparius was similar to Panicum virgatum [66], Maytenus emarginata [67] and Ziziphus mauritiana [68], which were analyzed by the same markers. But it was lower than microsatellite markers [34].…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure of Miscanthus lutarioriparius, an endemic plant of China

et al. 2019

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Miscanthus lutarioriparius is a native perennial Miscanthus species of China, which is currently used as raw material of papermaking and bioenergy crop. It also has been considered as a promising eco-bioindustrial plant, which can offer raw material and gene for the biomass industry. However, lack of germplasm resources and genetic diversity information of M. lutarioriparius have become the bottleneck that prevents the stable and further development of the biomass industry. In the present study, genetic diversity of 153 M. lutarioriparius individuals nine populations was studied using 27 Start Codon Targeted (SCoT) markers. High polymorphic bands (97.67%), polymorphic information content (0.26) and allele number (1.88) showed SCoT as a reliable marker system for genetic analysis in M. lutarioriparius. At the species, the percentage of polymorphic loci [PPL] was 97.2%, Nei’s gene diversity [H] was 0.36, Shannon index [I] was 0.54 and Expected Heterozygosity [He] was 0.56. Genetic variation within populations (84.91%) was higher than among populations (15.09%) based on analysis of molecular variance (AMOVA). Moderate level of genetic differentiation was found in M. lutarioriparius populations (Fst = 0.15), which is further confirmed by STRUCTURE, principal coordinates analysis (PCoA) and an unweighted pair group method with arithmetic mean (UPGMA) analysis that could reveal a clear separation between groups of the north and south of Yangtze River. The gene flow of the populations within the respective south and north of Yangtze River area was higher, but lower between the areas. There was no obvious correlation between genetic distance and geographic distance. The breeding systems, geographical isolation and fragmented habitat of M. lutarioriparius may be due to the high level of genetic diversity, moderate genetic differentiation, and the population, structure. The study further suggests some measure for conservation of genetic resources and provides the genetic basis for improving the efficiency of breeding based on the results of diversity analysis.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure of Miscanthus lutarioriparius, an endemic plant of China

et al. 2019

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“…ISSR marker has been widely used in the fields of germplasm collection, genetic diversity, genetic mapping and marker assisted selection (Levi et al, 2006;Zhang et al, 2011;Sunar et al, 2016;Cui et al, 2017;Kumar and Roy, 2018). Few studies have focused on elucidating the complex genetic relationships among different jujube varieties by ISSR markers (Singh et al, 2017). In the present study, the genetic diversity of a wide variety of jujube germplasm resources was evaluated, which provides an important scientific basis for the efficient use of these germplasms.…”

Section: Discussionmentioning

confidence: 98%

Genetic Diversity and Population Structure of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) and Sour Jujube (<i>Ziziphus acidojujuba</i> Mill.) using Inter-simple Sequence Repeat (ISSR) Markers

Li¹,

Guo²,

Tian³

et al. 2021

mpb

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The Chinese jujube (Ziziphus jujuba Mill.) originates from sour jujube (Ziziphus acidojujuba Mill.) and is an economically important genus in the Rhamnaceae family. However, little is known about the genetic relationship between jujube cultivars and wild species. In this study, we estimated the genetic variation and relationships between 85 jujube cultivars and 55 sour jujube individuals by ISSR markers. Of 216 ISSR primers, 110 were able produce amplified product(s) and 28 showed polymorphisms, accounting for 50.9% and 25.5% of total primers respectively. A total of 89 amplicons were amplified with 28 primers, of which 42 amplicons (47.2%) were polymorphic, and most of primers exhibited high PIC values. Cluster analysis and population structure analysis roughly divided the 140 accessions into two major groups. One group included all jujube cultivars and some sour jujube individuals, and the other group included remaining sour jujube individuals. Most jujube cultivars have a weak correlation with their origin, and there are obvious gene exchanges between sour jujube and jujube cultivars. The results provide a useful basis for jujube germplasm conservation, genetic improvement and evolution research.

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“…Currently, different types of molecular markers based on DNA polymorphism has been used for the assessment of genetic diversity in the plant species. Singh, Chhajer, Pathak, Bhatt, and Kalia (2017) had analyzed the genetic variation and relationships among 37 cultivars of Ziziphus mauritiana native of India using start codon targeted (SCoT), inter-simple sequence repeats (ISSR), and ribosomal DNA (rDNA) markers. Genotyping-by-sequencing was used to detect and genotype single nucleotide polymorphisms (SNPs) in core of 130 Chinese jujube accessions and to further characterize their genetic diversity, population structure, and linkage disequilibrium (Chen, Hou, Zhang, Pang, & Li, 2017).…”

Section: Crop Sciencementioning

confidence: 99%

Assessment of genetic diversity in Ziziphus jujube Mill. Cultivars derived from northern China using inter‐simple sequence repeat markers

et al. 2020

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There are abundant germplasm resources for Chinese jujube (Ziziphus jujuba Mill.), particularly in northern China. This study intended to assess the relationships and genetic structure of 48 cultivars of jujube derived from seven geographical regions in northern China using inter‐simple sequence repeat (ISSR) markers. Eight ISSR primers were selected for determining the genetic diversity of the 48 jujube cultivars, resulting in the amplification of 110 polymorphic bands. The average number of polymorphic bands for the ISSR primers was 13.8 and percentage of polymorphic bands was 86.8%. By analysis of the population genetic structure, the 48 cultivars were classified into two groups, with two homogeneous gene pools according to a Bayesian method. One group was comprised of cultivars from Central Shanxi, Shandong, Hebei, and Henan, while the other group included cultivars from southern Shanxi, Beijing, Shaanxi, Gansu, Shandong, Hebei, and Henan. Unweighted pair‐group method with arithmetic means cluster analysis also indicated two groups with similarity coefficients ranging from .58–.93. In some subgroups, there was a correlation between the genetic relationships among cultivars and their origins, but no relationship between genetic relatedness and cultivar uses. Analysis of molecular variance revealed that 88% of the genetic variation was attributable to variation within populations. Our results provide a considerable amount of polymorphism data in 48 Chinese jujube cultivars, which may serve as a good foundation for further analysis of the correlations between phenotypic and genetic data in Chinese jujube.

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Genetic diversity of Indian jujube cultivars using SCoT, ISSR, and rDNA markers

Cited by 25 publications

References 40 publications

Genetic diversity and population structure of Miscanthus lutarioriparius, an endemic plant of China

Genetic diversity and population structure of Miscanthus lutarioriparius, an endemic plant of China

Genetic Diversity and Population Structure of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) and Sour Jujube (<i>Ziziphus acidojujuba</i> Mill.) using Inter-simple Sequence Repeat (ISSR) Markers

Assessment of genetic diversity in Ziziphus jujube Mill. Cultivars derived from northern China using inter‐simple sequence repeat markers

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