Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica with their transferability analysis to gramineae and non- gramineae species

AbstractSSR markers are commonly used for many genetic applications, such as map construction, fingerprinting and genetic diversity analysis due to their high reproducibility, levels of polymorphism and abundance. As endogenous, small RNAs, miRNAs have essential roles in plant development and gene expression under diverse stress conditions, including various biotic and abiotic stress conditions. In the present study, we predicted 110 pre-miRNAs sequences from 287 precursor miRNAs and used them as queries for SSR marker development. Among 110 primer pairs, 85 were successfully amplified and examined for transferability to other gramineae and non-gramineae species. The results showed that all 82 primer pairs yielded unambiguous and strong amplification, and across the 23 studied Cleistogenes accessions, a total of 385 alleles were polymorphic. The number of alleles produced per primer varied from 3 to 11, with an average of 4.69 per locus. The expected heterozygosity (He) ranged from 0.44 to 0.88, with an average of 0.74 per locus, and the PIC (Polymorphism Information Content) values ranged from 0.34 to 0.87, with an average of 0.69 per locus. In this study, 1422 miRNA target genes were predicted and analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. The results showed that this miRNA-based microsatellite marker system can be very useful for genetic diversity and marker-assisted breeding studies.

Download Full-text

Genome-wide SSR Markers in Bottle Gourd: Development, Characterization, Utilization in Assessment of Genetic Diversity of National Genebank of India and Synteny With Other Related Cucurbits

10.21203/rs.3.rs-990222/v1 ◽

2021 ◽

Author(s):

Bhawna Bonthala ◽

Manjusha Verma ◽

M Z Abdin ◽

Lalit Arya ◽

Chithra D Pandey ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Bottle Gourd ◽

Map Construction ◽

Phylogenetic Studies ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome ◽

Tetranucleotide Repeats ◽

Nucleotide Repeats

Abstract Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, flower and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance,informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding geneticimprovement, cultivar identification and phylogenetic studies. Next generation sequencing has revolutionizedthe approaches for discovery, assessment and validation of molecular markers. We conducted a genome wideanalysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data.By performing in silico mining of microsatellite repeat-motifs, we developed 45,066 perfect SSR markers. Ofwhich 203 markers were successfully validated and 101 (49.75%) polymorphic primer pairs were utilized for anin depth genetic diversity and population structure analysis of 96 accessions from the National Genebank ofIndia. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%),further 21.03%, 9.6% and 4.3% of di-, penta- and hexa- nucleotide repeats in the bottle gourd genome. Syntenyof SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber(93.2%), 12 chromosomes of melon (87.4%) and 11 watermelon (90.8%). The generated SSR markers providea valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, genediscovery and for breeding in bottle gourd and other cucurbits species.

Download Full-text

Genetic Diversity of Selected Rice Genotypes under Water Stress Conditions

Plants ◽

10.3390/plants10010027 ◽

2020 ◽

Vol 10 (1) ◽

pp. 27

Author(s):

Mahmoud M. Gaballah ◽

Azza M. Metwally ◽

Milan Skalicky ◽

Mohamed M. Hassan ◽

Marian Brestic ◽

...

Keyword(s):

Genetic Diversity ◽

Water Stress ◽

Drought Stress ◽

Drought Tolerance ◽

Ssr Markers ◽

Similarity Index ◽

Stress Conditions ◽

Yield Potential ◽

Drought Tolerant ◽

Rice Genotypes

Drought is the most challenging abiotic stress for rice production in the world. Thus, developing new rice genotype tolerance to water scarcity is one of the best strategies to achieve and maximize high yield potential with water savings. The study aims to characterize 16 rice genotypes for grain and agronomic parameters under normal and drought stress conditions, and genetic differentiation, by determining specific DNA markers related to drought tolerance using Simple Sequence Repeats (SSR) markers and grouping cultivars, establishing their genetic relationship for different traits. The experiment was conducted under irrigated (normal) and water stress conditions. Mean squares due to genotype × environment interactions were highly significant for major traits. For the number of panicles/plants, the genotypes Giza179, IET1444, Hybrid1, and Hybrid2 showed the maximum mean values. The required sterility percentage values were produced by genotypes IET1444, Giza178, Hybrid2, and Giza179, while, Sakha101, Giza179, Hybrid1, and Hybrid2 achieved the highest values of grain yield/plant. The genotypes Giza178, Giza179, Hybrid1, and Hybrid2, produced maximum values for water use efficiency. The effective number of alleles per locus ranged from 1.20 alleles to 3.0 alleles with an average of 1.28 alleles, and the He values for all SSR markers used varied from 0.94 to 1.00 with an average of 0.98. The polymorphic information content (PIC) values for the SSR were varied from 0.83 to 0.99, with an average of 0.95 along with a highly significant correlation between PIC values and the number of amplified alleles detected per locus. The highest similarity coefficient between Giza181 and Giza182 (Indica type) was observed and are susceptible to drought stress. High similarity percentage between the genotypes (japonica type; Sakha104 with Sakha102 and Sakha106 (0.45), Sakha101 with Sakha102 and Sakha106 (0.40), Sakha105 with Hybrid1 (0.40), Hybrid1 with Giza178 (0.40) and GZ1368-S-5-4 with Giza181 (0.40)) was also observed, which are also susceptible to drought stress. All genotypes are grouped into two major clusters in the dendrogram at 66% similarity based on Jaccard’s similarity index. The first cluster (A) was divided into two minor groups A1 and A2, in which A1 had two groups A1-1 and A1-2, containing drought-tolerant genotypes like IET1444, GZ1386-S-5-4 and Hybrid1. On the other hand, the A1-2 cluster divided into A1-2-1 containing Hybrid2 genotype and A1-2-2 containing Giza179 and Giza178 at coefficient 0.91, showing moderate tolerance to drought stress. The genotypes GZ1368-S-5-4, IET1444, Giza 178, and Giza179, could be included as appropriate materials for developing a drought-tolerant variety breeding program. Genetic diversity to grow new rice cultivars that combine drought tolerance with high grain yields is essential to maintaining food security.

Download Full-text

Genetic Diversity of Angelica gigas Nakai Collected in Korea using Genome-Wide SSR Markers

Korean Journal of Medicinal Crop Science ◽

10.7783/kjmcs.2019.27.6.376 ◽

2019 ◽

Vol 27 (6) ◽

pp. 376-382

Author(s):

Dae Hui Jeong ◽

Yun Mi Park ◽

Ki Yoon Kim ◽

Hong Woo Park ◽

Kwon Seok Jeon ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Angelica Gigas ◽

Angelica Gigas Nakai ◽

Genome Wide

Download Full-text

Genome-wide identification of SSR markers in the Brassica A genome and their utility in breeding

Canadian Journal of Plant Science ◽

10.1139/cjps-2015-0250 ◽

2016 ◽

Vol 96 (5) ◽

pp. 808-818 ◽

Cited By ~ 4

Author(s):

Neil Hobson ◽

Habibur Rahman

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Low Cost ◽

Pak Choi ◽

Genome Wide ◽

A Genome ◽

Wide Range ◽

Genetic Pools ◽

High Level ◽

Simple Sequence

Simple sequence repeat (SSR) markers can be applied to genotyping projects at low cost with inexpensive equipment. The objective of this study was to develop SSR markers from the publically-available genome sequence of Brassica rapa and provide the physical position of these markers on the chromosomes for use in breeding and research. To assess the utility of these new markers, a subset of 60 markers were used to genotype 43 accessions of B. rapa. Fifty-five markers from the 10 chromosome scaffolds produced a total of 730 amplicons, which were then used to perform a phylogenetic analysis of the accessions, illustrating their utility in distinguishing between a wide range of germplasm. In agreement with similar studies of genetic diversity, our markers separated accessions into distinct genetic pools including Chinese cabbage, Chinese winter oilseed, European winter oilseed, Canadian spring oilseed, pak-choi, turnip, and yellow sarson. The results further illustrate the presence of a high level of genetic diversity in B. rapa, and demonstrate the potential of these SSR markers for use in breeding and research.

Download Full-text

Molecular characterization of almond accessions from the island of La Palma (Canary Islands, Spain) using SSR markers

Plant Genetic Resources ◽

10.1017/s1479262114000112 ◽

2014 ◽

Vol 12 (3) ◽

pp. 323-329 ◽

Cited By ~ 1

Author(s):

Guillermo Padilla ◽

Rafel Socias i Company ◽

Amando Ordás

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Average Value ◽

La Palma ◽

Expected Heterozygosity ◽

Commercial Cultivars ◽

Soft Shell ◽

Genetic Profiles ◽

Simple Sequence

In this study, 15 simple sequence repeat (SSR) markers were used for genetic diversity analysis of 45 almond accessions, which included 25 local cultivars from La Palma Island and three other commercial cultivars. A total of 110 amplification fragments were produced, with an average value of 7.9 alleles per locus. Twelve of the SSR markers can be considered as highly informative, with values of expected heterozygosity and power of discrimination above 0.5 and 0.8, respectively. Due to cases of synonymy and homonymy, 37 different genetic profiles were obtained, with the homonymy of the soft-shell varieties known as ‘Mollar’ being the most significant. Cluster analysis identified four groups within the accessions. One of these groups exclusively consisted of the two commercial cultivars ‘Guara’ and ‘Ferraduel’. The other commercial cultivar used in the study, ‘Desmayo Largueta’, was in a cluster with three cultivars from the same locality. The analysis of molecular variance revealed that the within-localities component accounts for most of the total variation, suggesting that La Palma almond cultivars did not originate independently in different parts of the island. The results of the study reveal the genetic singularity of La Palma almond cultivars and the genetic diversity among them.

Download Full-text

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.

Download Full-text

Genetic diversity of walnut (Juglans regia L.) seedlings through SSR markers in north-western Himalayan region of Jammu

Bangladesh Journal of Botany ◽

10.3329/bjb.v49i4.52517 ◽

2020 ◽

Vol 49 (4) ◽

pp. 1003-1012

Author(s):

Rafiq Ahmad Shah ◽

Parshant Baksi ◽

Amit Jasrotia ◽

Deep JI Bhat ◽

Rucku Gupta ◽

...

Keyword(s):

Genetic Diversity ◽

Decision Making ◽

Ssr Markers ◽

Juglans Regia ◽

Germplasm Management ◽

Expected Heterozygosity ◽

Western Himalayan Region ◽

Ssr Primers ◽

Genetic Dissimilarity ◽

North Western

screening of 25 SSR markers, revealed 23 clear and consistent amplification profiles in the entire walnut germplasm set. A total of 54 alleles were amplified by SSR primers and the number of alleles range from 2 to 3. The PIC value ranged from 0.36 to 0.68. The dendrogram classified all genotypes into two main clusters with various degrees of subclustering. Estimated genetic dissimilarity coefficient ranged from 0.36 to 0.85. Through model-based cluster analysis all genotypes were grouped into 5 genetically distinct subpopulations. The expected heterozygosity at a given locus was found to range from 0.520 to 0.5477. Similarly, population differentiation measurements (Fst) ranged from 0.2286 to 0.2909. These findings would be helpful for decision making in future walnut breeding studies, germplasm management activities to maximize genetic diversity in walnut germplasm and may also prove useful in future for conducting association mapping in walnut for different traits.

Download Full-text

Genetic diversity and population structure of pear (Pyrus spp.) collections revealed by a set of core genome-wide SSR markers

Tree Genetics & Genomes ◽

10.1007/s11295-015-0953-z ◽

2015 ◽

Vol 11 (6) ◽

Cited By ~ 21

Author(s):

Qingwen Liu ◽

Yue Song ◽

Lun Liu ◽

Mingyue Zhang ◽

Jiangmei Sun ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Core Genome ◽

Genome Wide

Download Full-text

Molecular characterization of China aster (Callistephus chinensis (L.) Nees) genotypes using SSR markers

Israel Journal of Plant Sciences ◽

10.1163/22238980-bja10037 ◽

2021 ◽

pp. 1-10

Author(s):

Veluru Bhargav ◽

Rajiv Kumar ◽

Anuradha Sane ◽

T. Manjunatha Rao ◽

T. Usha Bharathi ◽

...

Keyword(s):

Genetic Diversity ◽

Association Mapping ◽

Ssr Markers ◽

Crop Improvement ◽

Flower Color ◽

Target Populations ◽

Genome Wide ◽

China Aster ◽

Simple Sequence

Abstract Understanding genetic diversity in target populations is of great importance in breeding and a prerequisite for association mapping of traits. In this study, 57 cross species simple sequence repeat (SSR) markers were screened for amplification in China aster. Twenty six polymorphic markers were used to estimate the genetic diversity in forty two China aster genotypes. The observed and expected heterozygosities within the genotypes were ranged from 0.00 to 0.80 and 0.17 to 0.50, respectively. Weighted Neighbor Joining method, grouped China aster genotypes into five major clusters which coincided for morphological traits mostly flower color and form, but not correlated for their geographical locations. The results suggested that, population may be useful for the genome-wide marker–trait association mapping. These set of cross species transferable SSR markers would enable the application of the SSR technique in China aster crop improvement.

Download Full-text