Multi-locus DNA fingerprinting and genetic diversity in jute (Corchorus spp.) based on sequence-related amplified polymorphism

Rana, M. K.; Arora, Kashika; Singh, Sonika; Singh, Amit Kumar

doi:10.1007/s13562-012-0104-7

Cited by 20 publications

(7 citation statements)

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“…The high polymorphism rate in this study coincides with those obtained in other plant species including 90% and 96.1% in alfalfa [24,25], 95% in buffalograss [36], 89% in jute [43], 87.59% in Musa [46], and 95.23% in Paeonia [47]. However, the polymorphic rate observed in this study was much higher than that generated using SRAP markers in other plant species, including 73.4% in cassava varieties [48], 56.0% in eggplant and related Solanum species [49], 47.2% and 72% in sesame [39,40], 81.97% in Pogostemon [50], 49.39% in Brassica juncea [51], 72.7% in Cucurbita pepo [52], 66.2% in Cucurbita moschata [35], 57% and 76.4% in safflower [41,42], 43% in Coffea arabica [45], 50% in Turkish okra [53], and 83% in sugarcane germplasm collections [37].…”

Section: Discussionsupporting

confidence: 90%

Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP) Markers in Vicia faba L.

Alghamdi

Al-Faifi

Migdadi

et al. 2012

IJMS

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Sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity and relationship among 58 faba bean (Vicia faba L.) genotypes. Fourteen SRAP primer combinations amplified a total of 1036 differently sized well-resolved peaks (fragments), of which all were polymorphic with a 0.96 PIC value and discriminated all of the 58 faba bean genotypes. An average pairwise similarity of 21% was revealed among the genotypes ranging from 2% to 65%. At a similarity of 28%, UPGMA clustered the genotypes into three main groups comprising 78% of the genotypes. The local landraces and most of the Egyptian genotypes in addition to the Sudan genotypes were grouped in the first main cluster. The advanced breeding lines were scattered in the second and third main clusters with breeding lines from the ICARDA and genotypes introduced from Egypt. At a similarity of 47%, all the genotypes formed separated clusters with the exceptions of Hassawi 1 and Hassawi 2. Group analysis of the genotypes according to their geographic origin and type showed that the landraces were grouped according to their origin, while others were grouped according to their seed type. To our knowledge, this is the first application of SRAP markers for the assessment of genetic diversity in faba bean. Such information will be useful to determine optimal breeding strategies to allow continued progress in faba bean breeding.

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Section: Discussionsupporting

confidence: 90%

Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP) Markers in Vicia faba L.

Alghamdi

Al-Faifi

Migdadi

et al. 2012

IJMS

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“…Of the 50 primers, 29 (58%) exhibited polymorphisms, similar to the amount of polymorphism exhibited in Citrullus lanatus (Liu et al 2016). The PIC value varied from 0.340 to 0.680 with an average of 0.491 implying that most InDels were within a moderate range of genetic diversity, which is consistent with the other types of markers in jute (Grabherr et al 2011;Rana et al 2013;Ghosh et al 2014). In addition, polymorphic InDel markers were successfully used in a cluster analysis of 62 jute accessions, which indicated that our main aim (the large-scale development of InDel markers) was successfully achieved.…”

Section: R a F Tsupporting

confidence: 56%

Development of an InDel polymorphism database for jute via comparative transcriptome analysis

Yang

Dai

Xie

et al. 2018

Genome

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Jute (Corchorus spp.) is one of the most commercially important bast fiber crops in the world. However, molecular markers and high-density genetic maps are still lacking on jute compared with other crops. Insertion/deletion (InDel) markers, one of the most abundant sources of DNA/RNA variations in plant genomes, can easily be distinguished among different accessions using high-throughput sequencing. Using three transcriptome datasets, we identified and developed InDel markers. Altogether, 51 172 InDel sites in 18 800 unigenes were discovered, and the number of InDel loci per unigene varied from 1 to 31. Further, we found 94 InDel types, varying from 1 to 159 bp; the most common were single-nucleotide (23 028), binucleotide (9824), and trinucleotide (9182). In total, 49 563 InDels in 18 445 transcripts were discovered in the comparison between TC and YG, followed by 48 934 InDels in 18 408 transcripts between NY and YG, and 3570 InDels in 2701 unigenes between NY and TC. Additionally, there were 1273 InDel sites in 1129 unigenes with polymorphisms between any two of the three accessions. Twenty-nine (58%) primer pairs represented polymorphisms when compared to the jute accessions, and PIC varied from 0.340 to 0.680, with an average of 0.491.

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“…It appeared to be simple, efficient and cost-effective. Typically, it specifically targeted to the genome open reading frame (ORF) sequences providing more genetic information associated with phenotype (Ferriol et al 2003;Uzun et al 2009;Castonguay et al 2010;Rana et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Genotypic variation of Cunninghamia lanceolata revealed by phenotypic traits and SRAP markers

Zheng

Duan

et al. 2015

Dendrobiology

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Abstract:The success of a tree breeding program largely depended on the available genetic variability of the germplasms. Our present study aimed to assess the phenotypic variation and DNA variability using sequence-related amplified polymorphism (SRAP) markers among 50 Cunninghamia lanceolata (Chinese fir) genotypes. Extensive phenotypic variations (p < 0.05 or 0.01) were found for all the growth and wood property traits (height, diameter at breast height, stem volume, and wood basic density, hygroscopicity, heart-wood ratio, tracheid length, tracheid diameter and tracheid length-diameter ratio) with coefficients of variation spanning from 6.8 to 31.3%. At the DNA level, thirty-five SRAP primer combinations produced 498 bands with 89.4% polymorphism across genotypes; moreover, the Nei's gene diversity was detected to be ranged between 0.204 and 0.373 (mean = 0.279), while the Shannon's Information Index stretched from 0.324 to 0.555 with an average value of 0.427. Significance (p < 0.01) of the variability of SRAP polymorphism among genotypes was further demonstrated by AMOVA. These results indicated a relatively high level of genetic diversity in genotypes. The SRAP' dendrogram additionally revealed that these genotypes could be split into 7 clusters with higher discriminating capacity over that of phenotype. Notably, a total of 99 statistically significant (p < 0.05) marker-trait associations related to the growth and wood property traits were identified. These marker-trait associations corresponded to 77 different SRAP markers with R 2 (percentage of the phenotypic variation explained by marker) ranging from 8.3 to 26.4%. Additional key words:Chinese fir, wood property, molecular marker, dendrogram and marker-trait association.

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Multi-locus DNA fingerprinting and genetic diversity in jute (Corchorus spp.) based on sequence-related amplified polymorphism

Cited by 20 publications

References 20 publications

Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP) Markers in Vicia faba L.

Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP) Markers in Vicia faba L.

Development of an InDel polymorphism database for jute via comparative transcriptome analysis

Genotypic variation of Cunninghamia lanceolata revealed by phenotypic traits and SRAP markers

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