Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)

Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine. A considerable extent of genetic diversity in ginger occurs in the Western Ghats and North-Eastern India. However, genetic diversity studies at the molecular level in ginger is limited due to limited availability of genetic and genomic information. In the present study, for the first time, we have identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from ginger. We obtained 16,790 EST-SSR loci from 78987 unigenes, and 4597 SSR loci in the predicted 76929 coding sequences from RNA-Seq assembled contigs of ginger through Illumina paired-end sequencing. Gene ontology results indicate that the unigenes with SSR loci participate in various biological processes such as metabolism, growth, and development in ginger. One hundred and twenty-five primer pairs were designed from unigenes and coding sequences. These primers were tested for PCR optimization, characterization, and amplification and identified 12 novel EST-SSR markers. Twelve flanking polymorphic EST-SSR primers were validated using 48 ginger genotypes representing North-Eastern India and different eco-geographical adaptations by PCR amplification and allele sizing through capillary electrophoresis. Twelve EST-SSR primers generated a total of 111 alleles with an average of 9.25 alleles per locus and allele sizes ranging between 115-189bp. This study implies that the SSR markers designed from transcriptome sequences provides ample EST-SSR resources, which are helpful for genetic diversity analysis of Zingiberaceae species and molecular verification of ginger genotypes.

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Evaluation of Genetic Diversity of Chilli Landraces from North Eastern India Based on Morphology, SSR Markers and the Pun1 Locus

Plant Molecular Biology Reporter ◽

10.1007/s11105-012-0466-y ◽

2012 ◽

Vol 30 (6) ◽

pp. 1470-1479 ◽

Cited By ~ 17

Author(s):

Julia S. Yumnam ◽

Wricha Tyagi ◽

Avinash Pandey ◽

N. Tombisana Meetei ◽

Mayank Rai

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Eastern India ◽

North Eastern ◽

North Eastern India

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Genome-wide development of lncRNA-derived-SSR markers for Dongxiang wild rice (Oryza rufipogon Griff.)

10.1101/2021.08.23.457289 ◽

2021 ◽

Cited By ~ 1

Author(s):

Wanling Yang ◽

Yuanwei Fan ◽

Yong Chen ◽

Gumu Ding ◽

Hu Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Stress Responses ◽

Wild Rice ◽

Diversity Index ◽

Oryza Rufipogon ◽

Coding Sequences ◽

Genome Wide ◽

Ssr Loci ◽

Dongxiang Wild Rice

AbstractDongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost distributed common wild rice found in the world. It contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in crop breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice materials. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content (PIC) values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research, including genetic diversity analysis, QTL mapping, and molecular breeding programs, to make good use of the elite lncRNA genes from DXWR.

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Genotypic and phenotypic dissection of Xanthomonas oryzae pv. oryzae on Indica rice cultivars for bacterial blight resistance

Journal of Environmental Biology ◽

10.22438/jeb/42/6/mrn-1156 ◽

2021 ◽

Vol 42 (6) ◽

pp. 1578-1590

Author(s):

J. Kumar ◽

◽

A. Hussain ◽

P. Singh ◽

S.K.Y. Baksh ◽

...

Keyword(s):

Genetic Diversity ◽

Bacterial Blight ◽

Indica Rice ◽

R Gene ◽

Rice Cultivars ◽

Eastern India ◽

Gene Combination ◽

North Eastern ◽

North Eastern India ◽

Blight Disease

Aim: To evaluate the level of virulence of different Xoo isolates/ pathotypes of Eastern and North-eastern India and to identify the suitable donors in rice cultivars having various R-gene combination against virulent Xoo races of Bacterial Blight disease of rice. Methodology: Thirty six Xoo isolates were collected from different places of Eastern and North-eastern India and genetic diversity/ similarity was examined by genotyping of pathotypes using JEL1/JEL2 markers. The 34 Indica rice cultivars carrying different R-gene combination were selected and grown in net house and inoculated artificially with Xoo inoculants from these races/ isolates bacterial of blight disease. Results: The selected 36 Xoo isolates of Eastern and North-eastern India were grouped into seven different isolates/ races based on their genetic diversity using JEL1/JEL2 markers. Among 34 Indica rice cultivars, three or more R-gene combination (xa5 + xa13 + Xa21 and/or Xa4 + xa5 + xa13 + Xa21) cultivars exhibited highly resistant as compared to cultivars with single and double gene combination cultivars against most of the Xoo isolates/ races. Interpretation: The cultivars may determine different level of resistance due to complementary effect of inheritance of suitable R-gene combination. Identified donors may be used for rice resistance breeding programme for Eastern and North-eastern India.

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Use of expressed sequence tag microsatellite markers for exploring genetic diversity in lentil and related wild species

The Journal of Agricultural Science ◽

10.1017/s0021859615001252 ◽

2016 ◽

Vol 154 (7) ◽

pp. 1254-1269 ◽

Cited By ~ 1

Author(s):

A. SINGH ◽

H. K. DIKSHIT ◽

D. SINGH ◽

N. JAIN ◽

M. ASKI ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Wild Species ◽

Expressed Sequence Tag ◽

Group Method ◽

Comparative Genomic ◽

Pair Group ◽

Ssr Loci ◽

Related Wild Species ◽

Expressed Sequence

SUMMARYExpressed sequence tag-simple sequence repeat (EST-SSR) markers were used to analyse genetic diversity among three Lens species. The SSR loci amplified successfully in wild species, with 94·82% transferability in Lens culinaris subsp. orientalis, 95·4% in Lens nigricans, 98·81% in L. culinaris subsp. odemensis, 94·82% in L. culinaris subsp. tomentosus and 96·55% in Lens ervoides. Ninety-nine alleles (average 3·41 alleles/locus) were detected by 29 SSR markers. Based on the unweighted pair group method with arithmetic mean cluster analysis, all the genotypes were grouped into three clusters at a similarity level of 0·30. The diversity analysis indicated no species-specific clustering of the wild and cultivated species. Wild species L. nigricans and L. culinaris subsp. odemensis, L. culinaris subsp. orientalis and L. ervoides were grouped in Cluster I, whereas the Mediterranean land races of L. culinaris subsp. culinaris and L. culinaris subsp. tomentosus formed a separate group in Cluster II A. Cluster II B comprised L. ervoides, L. culinaris subsp. orientalis and L. culinaris subsp. culinaris. Clusters II C, II D and II F included cultivated Indian lentil genotypes. Cluster II E comprised Indian and Mediterranean germplasm lines. Cluster II F included three early maturing germplasm lines, whereas Cluster III included only two germplasm lines. The functional annotation of SSR-containing unigenes revealed that a majority of genes were involved in an important transport-related function or were a component of metabolic pathways. A high level of polymorphism of EST-SSRs and their transferability to related wild species indicated that these markers could be used for molecular screening, map construction, comparative genomic studies and marker-assisted selection.

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Genetic diversity of Crotalaria germplasm assessed through phylogenetic analysis of EST-SSR markers

Genome ◽

10.1139/g06-027 ◽

2006 ◽

Vol 49 (6) ◽

pp. 707-715 ◽

Cited By ~ 15

Author(s):

M L Wang ◽

J A Mosjidis ◽

J B Morris ◽

R E Dean ◽

T M Jenkins ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Ssr Markers ◽

Expressed Sequence Tag ◽

Germplasm Collection ◽

High Similarity ◽

Ssr Primers ◽

Expressed Sequence ◽

Simple Sequence ◽

Crotalaria Spectabilis

The genetic diversity of the genus Crotalaria is unknown even though many species in this genus are economically valuable. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago and soybean were used to assess the genetic diversity of the Crotalaria germplasm collection. This collection consisted of 26 accessions representing 4 morphologically characterized species. Phylogenetic analysis partitioned accessions into 4 main groups generally along species lines and revealed that 2 accessions were incorrectly identified as Crotalaria juncea and Crotalaria spectabilis instead of Crotalaria retusa. Morphological re-examination confirmed that these 2 accessions were misclassified during curation or conservation and were indeed C. retusa. Some amplicons from Crotalaria were sequenced and their sequences showed a high similarity (89% sequence identity) to Medicago truncatula from which the EST-SSR primers were designed; however, the SSRs were completely deleted in Crotalaria. Highly distinguishing markers or more sequences are required to further classify accessions within C. juncea.Key words: Crotalaria germplasm, EST-SSR, genetic diversity, phylogeny.

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Analysis of genetic diversity and population structure in Capsicum landraces from North Eastern India using TE-AFLP markers

Plant Molecular Biology Reporter ◽

10.1007/s11105-015-0968-5 ◽

2016 ◽

Vol 34 (4) ◽

pp. 869-875 ◽

Cited By ~ 5

Author(s):

Md Aminul Islam ◽

Pratima Sinha ◽

Shyam Sundar Sharma ◽

Madan Singh Negi ◽

Bijoy Neog ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Aflp Markers ◽

Eastern India ◽

North Eastern ◽

North Eastern India

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Development and Characterization of Simple Sequence Repeat Markers for, and Genetic Diversity Analysis of Liquidambar formosana

Forests ◽

10.3390/f11020203 ◽

2020 ◽

Vol 11 (2) ◽

pp. 203

Author(s):

Siyuan Chen ◽

Mingliang Dong ◽

Yan Zhang ◽

Shuaizheng Qi ◽

Xuezeng Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tag ◽

Genomic Analysis ◽

Deciduous Tree ◽

Genetic Studies ◽

Ssr Loci ◽

Nonspecific Amplification ◽

Close Relatives ◽

Simple Sequence

Liquidambar formosana (Hamamelidaceae) is a relatively fast-growing deciduous tree of high ornamental value that is indigenous to China. However, few molecular markers are available for the species or its close relatives; this has hindered genomic and genetic studies. Here, we develop a series of transferable expressed sequence tag-simple sequence repeats (EST-SSRs) for genomic analysis of L. formosana. We downloaded the sequence of the L. formosana transcriptome from the National Center of Biotechnology Information Database and identified SSR loci in the Unigene library. We found 3284 EST-SSRs by mining 34,491 assembled unigenes. We synthesized 100 random primer pairs for validation of eight L. formosana individuals; of the 100 pairs, 32 were polymorphic. We successfully transferred 12 EST-SSR markers across three related Liquidambar species; the markers exhibited excellent cross-species transferability and will facilitate genetic studies and breeding of Liquidambar. A total of 72 clones of three Liquidambar species were uniquely divided into three main clusters; principal coordinate analysis (PCoA) supported this division. Additionally, a set of 20 SSR markers that did not exhibit nonspecific amplification were used to genotype more than 53 L. formosana trees. The mean number of alleles (Na) was 5.75 and the average polymorphism information content (PIC) was 0.578, which was higher than that of the natural L. formosana population (0.390). In other words, the genetic diversity of the plus L. formosana population increased, but excellent phenotypic features were maintained. The primers will be valuable for genomic mapping, germplasm characterization, gene tagging, and further genetic studies. Analyses of genetic diversity in L. formosana will provide a basis for efficient application of genetic materials and rational management of L. formosana breeding programs.

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