Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding

Saha, Dipnarayan; Rana, R. S.; Chakraborty, Sukla; Datta, Subhojit; Kumar, Amrendra; Chakraborty, Asim Kumar; Karmakar, P. G.

doi:10.1016/j.cj.2017.02.006

Cited by 37 publications

(9 citation statements)

References 41 publications

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“…These three types accounted for more than 79 % of all InDels. Furthermore, we compared the nucleotide composition of these three InDel types (Table S5) Currently, most molecular markers used in jute are RAPDs, SRAPs, ISSRs, and SSRs (Das et al 2012;Zhang et al 2015a;Zhang et al 2016;Saha et al 2017), and the number of markers based on PCR are limited. Further, the majority of jute molecular markers comprise 1,906 EST-SSR markers developed by Zhang et al, which is far from meeting the need for high-density genetic map construction and gene mapping for molecular markers.…”

Section: R a F Tmentioning

confidence: 99%

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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Section: R a F Tmentioning

confidence: 99%

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

Yang

Dai

Xie

et al. 2018

Genome

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“…Research on peanut (Bosamia et al 2015) yielded similar results regarding allele number as our study on C. alismatifolia. The CT motif was the most common SSR motif in C. alismatifolia, as also observed in Hevea brasiliensis (Li et al 2012) and Corchorus capsularis (Saha et al 2017). In contrast, the AT motif was found to be most common for Cryptomeria japonica (Ueno et al 2012), and AAG was most common for Arachis hypogaea (Bosamia et al 2015).…”

Section: Discussionmentioning

confidence: 53%

Development of SSR markers and their application to genetic diversity analysis of Curcuma alismatifolia varieties

Mao¹,

Liu

Ding³

et al. 2020

Bot. Sci.

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Background: Curcuma alismatifolia is an ornamental cultivar with several varieties introduced into China from Thailand within the past fifteen years. Curcuma alismatifolia is widely used as cut flowers and potted flowers and is also used in flower beds. Questions and/or Hypotheses: However, limited genetic and genomic information is available for this species, which has impeded studies on the enhancement of its ornamental value and stress resistance. Studied species Curcuma alismatifolia Study site and dates: Zhejiang, 2018 Methods: single-cell sequencing technology of PCR and polyacrylamide gel electrophoresis Results: (A/T)n accounted for 43.6 % of the SSRs, the maximum proportion, and mononucleotide and trinucleotide repeats were the two most abundant repeat types. A total of 3,637 primer pairs flanking SSR sequences were successfully designed, and 70 sets of primers were randomly selected for validation in 10 varieties. Forty-one (59 %) of the 70 primer pairs successfully amplified alleles, of which 35 were identified as polymorphic markers and used to assess the level of genetic diversity and genetic relationships among the 10 varieties. The genetic diversity analysis showed that the number of alleles (Na) at each locus ranged from 2 to 8, with an average of 3.97, and that PIC had a mean of 0.524 and ranged from 0.095 to 0.795. Conclusions: The genetic distance between 10 varieties varied from 0.30 to 0.96, and the dendrogram clustered all varieties into three groups.

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“…Moreover, SSR polymorphisms are employed to identify and characterize germplasm resources in terms of affiliation ( Tuler et al, 2015 ), and the development and characterization of genomic SSRs in hemp are important to enable genetic research and marker-assisted selection. Because SSR markers have a higher number of polymorphisms than other molecular markers, they are popular and ideal for analyzing population structure and genetic diversity and identifying fiber crop varieties ( Zhang et al, 2015a , b ; Saha et al, 2017 , 2019 ). In previous research, EST-SSR development was conducted, and 4577 potential SSR motifs were identified for Cannabis ( Gao et al, 2014 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Cannabis Based on the Genome-Wide Development of Simple Sequence Repeat Markers

et al. 2020

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Cannabis has been used as a source of nutrition, medicine, and fiber. However, lack of genomic simple sequence repeat (SSR) markers had limited the genetic research on Cannabis species. In the present study, 92,409 motifs were identified, and 63,707 complementary SSR primer pairs were developed. The most abundant SSR motifs had six repeat units (36.60%). The most abundant type of motif was dinucleotides (70.90%), followed by trinucleotides, tetranucleotides, and pentanucleotides. We randomly selected 80 pairs of genomic SSR markers, of which 69 (86.25%) were amplified successfully; 59 (73.75%) of these were polymorphic. Genetic diversity and population structure were estimated using the 59 (72 loci) validated polymorphic SSRs and three phenotypic markers. Three hundred ten alleles were identified, and the major allele frequency ranged from 0.26 to 0.85 (average: 0.56), Nei’s genetic diversity ranged from 0.28 to 0.82 (average: 0.56), and the expected heterozygosity ranged from 0.28 to 0.81 (average: 0.56). The polymorphism information content ranged from 0.25 to 0.79 (average: 0.50), the observed number of alleles ranged from 2 to 8 (average: 4.13), and the effective number of alleles ranged from 0.28 to 0.81 (average: 0.5). The Cannabis population did not show mutation-drift equilibrium following analysis via the infinite allele model. A cluster analysis was performed using the unweighted pair group method using arithmetic means based on genetic distances. Population structure analysis was used to divide the germplasms into two subgroups. These results provide guidance for the molecular breeding and further investigation of Cannabi s.

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Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding

Cited by 37 publications

References 41 publications

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

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

Development of SSR markers and their application to genetic diversity analysis of Curcuma alismatifolia varieties

Genetic Diversity and Population Structure of Cannabis Based on the Genome-Wide Development of Simple Sequence Repeat Markers

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