Evaluation of the number and information content of fluorescent-labeled SSR markers for rice germplasm characterization

A chickpea simple sequence repeat (SSR) marker reference kit has been developed based on the genotyping of the global chickpea composite collection (3,000 accessions) with 35 SSR markers. The kit consists of three pools of chickpea accessions along with supporting documentation on the SSR markers, polymerase chain reaction and detection conditions, and the expected allele sizes for each of the 35 SSR loci. These markers were selected based on quality criteria, genome coverage and locus-specific information content. Other important SSR selection criteria were quality of amplification products, locus complexity, polymorphism information content and well-dispersed location on a chickpea genetic map. The developed SSR kit has a wide range of applications, especially for genetic diversity studies in chickpea. Using the markers and reference accessions in the kit, scientists in other laboratories will be able to compare the genotypic data that they obtain for their germplasm with that obtained using the global composite collection.

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Genetic variability in trait-specific rice germplasm groups based on coefficient of parentage, SSR markers and fertility restoration

Plant Genetic Resources ◽

10.1017/s147926211400063x ◽

2014 ◽

Vol 13 (1) ◽

pp. 56-67

Author(s):

Pawan Khera ◽

Akhilesh Kumar Singh ◽

Rahul Priyadarshi ◽

Durga Khandekar ◽

Rajani K Allu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Hybrid Rice ◽

Fertility Restoration ◽

Phenotypic Traits ◽

Rice Breeding ◽

Coefficient Of Parentage ◽

Rice Germplasm ◽

Cms Line ◽

The Mean

To maximize heterosis, it is important to understand the genetic diversity of germplasm and associate useful phenotypic traits such as fertility restoration for hybrid rice breeding. The objectives of the present study were to characterize genetic diversity within a set of rice germplasm groups using coefficient of parentage (COP) values and 58 simple sequence repeat (SSR) markers for 124 genotypes having different attributes such as resistance/tolerance to various biotic and abiotic stresses. These lines were also used for identifying prospective restorers and maintainers for wild abortive-cytoplasmic male sterile (CMS) line. The mean COP value for all the lines was 0.11, indicating that the genotypes do not share common ancestry. The SSR analysis generated a total of 268 alleles with an average of 4.62 alleles per locus. The mean polymorphism information content value was 0.53, indicating that the markers selected were highly polymorphic. Grouping based on COP analysis revealed three major clusters pertaining to the indica, tropical japonica and japonica lines. A similar grouping pattern with some variation was also observed for the SSR markers. Fertility restoration phenotype based on the test cross of the 124 genotypes with a CMS line helped identify 23 maintainers, 58 restorers and 43 genotypes as either partial maintainers or partial restorers. This study demonstrates that COP analysis along with molecular marker analysis might encourage better organization of germplasm diversity and its use in hybrid rice breeding. Potential restorers identified in the study can be used for breeding high-yielding stress-tolerant medium-duration rice hybrids, while maintainers would prove useful for developing new rice CMS lines.

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Assessment of Genetic Diversity in Rice Germplasm (Oryza sativa L.) using SSR Markers

International Journal of Current Microbiology and Applied Sciences ◽

10.20546/ijcmas.2020.905.398 ◽

2020 ◽

Vol 9 (5) ◽

pp. 3346-3355

Author(s):

Akhand Pratap ◽

Prashant Bisen ◽

Bapsila Loitongbam ◽

Sanket R. Rathi ◽

Pragya Parmita ◽

...

Keyword(s):

Genetic Diversity ◽

Oryza Sativa ◽

Ssr Markers ◽

Oryza Sativa L ◽

Rice Germplasm

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Assessment of diversity of Indian aromatic rice germplasm collections for morphological, agronomical, quality traits and molecular characters to identify a core set for crop improvement

CABI Agriculture and Bioscience ◽

10.1186/s43170-020-00013-8 ◽

2020 ◽

Vol 1 (1) ◽

Author(s):

G. S. V. Prasad ◽

G. Padmavathi ◽

K. Suneetha ◽

M. S. Madhav ◽

K. Muralidharan

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Crop Improvement ◽

Chromosome 6 ◽

Aromatic Rice ◽

Quality Traits ◽

Combined Analysis ◽

The Core ◽

Rice Germplasm ◽

Core Set

Abstract Background Besides the Basmati, the aromatic rice germplasm (ARG) accessions are treasured for quality, medicinal value and aroma. The demand for aromatic rice is ever increasing. Genetic diversity is the source of variability to identify superior alleles controlling morphological, agronomic and quality traits, and molecular attributes. This study reports on the characterization of traits in ARG to identify a core set for breeding high-yielding varieties. Methods The genetic diversity was measured on the distinctness, uniformity and stability (DUS) of 46 traits in 208 Indian ARG in field, greenhouse and laboratory tests. We performed individual and combined analysis of DUS traits and molecular data generated using 55 SSR markers. The genetic distances between genotypes were estimated using Mahalanobis D2 analysis and clustering by standardized Euclidean2 distances, Ward Minimum variance, Gowers’ similarity index and PowerMarker. The aim was to derive a core set of non-Basmati ARG using PowerCore to deploy in crop improvement. Results Eighty-two alleles were detected. Alleles per marker ranged from 2 (RM505) to 5 (RM276) with an average of 3.04 alleles. The markers are informative in analyzing the diversity as the PIC values estimated varied from 0.17 (RM577 on chromosome 1) to 0.72 (RM276 on chromosome 6) with an average of 0.54 per locus. RM276 with repeat motif of (AG)8A3(GA) 33 on chromosome 6 was the most informative (amplified 5 alleles). The combined analysis had shown genotypes in a few clusters to be more diverse than others. SSR markers RM289, RM505, RM577 and RM22866 were identified as genotype specific markers. With PowerCore, 46 genotypes (22%) were identified as a core set of ARG that represent all the alleles detected in the entire set investigated. 2-Acetyl-1-pyrroline is considered to impart aroma; it was not detected by GC–MS tests in many ARG. Conclusions Forty-six genotypes in the core set have different maturity periods, plant statures, grain types and grain quality traits. A parent can be selected from the core set to improve aromatic rice depending on the breeding objective. The olfactory sensing of strong aroma emitted by cooked kernels of all ARG was found more decisive than the costly GC–MS tests.

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Transferability of newly developed genomic lentil SSR markers to Cicer species

Legume Research - An International Journal ◽

10.18805/lr-466 ◽

2019 ◽

Author(s):

Melike Bakır

Keyword(s):

Microsatellite Markers ◽

Information Content ◽

Ssr Markers ◽

Lens Culinaris ◽

Polymorphic Information Content ◽

Research Infrastructure ◽

Great Effort ◽

Average Value ◽

Cicer Species ◽

Ssr Primers

Development of microsatellite markers requires a great effort, expertise and research infrastructure. Therefore, cross genera or species transferability of already developed markers has constituted a significant alternative. In this study, transferability of newly developed 53 genomic lentil (Lens culinaris Medik.) SSR markers to 32 accessions of Cicer species including C. arietinum L., C. bijugum K.H. Rech., C. echinospermum P.H. Davis, C. reticulatum Ladiz., C. pinnatifidium Jaub. and Sp., C. anatolicum Alef. was investigated. Of these markers, 33.09% were found to be transferrable to C. arietinum, 37.7% to C. echinospermum, 35.8% to C.reticulatum, 39.6% to C. bijugum, 18.8% to C. pinnatifidium and finally 15.09% to C. anatolicum species. From these markers, 11.3% were found to be transferable to all Cicer species. Transferable 6 polymorphic SSR primers had 19 alleles in 32 accessions with a mean of 3.16 alleles per locus. Polymorphic information content (PIC) values varied between 0.375 (Lc_MCu21) and 0.587 (Lc_MCu53) with an average value of 0.528. Transferable SSR markers were thought to provide significant contributions to inter and intra-specific studies in Cicer species.

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Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

BioMed Research International ◽

10.1155/2018/7658032 ◽

2018 ◽

Vol 2018 ◽

pp. 1-11 ◽

Cited By ~ 20

Author(s):

Saba Jasim Aljumaili ◽

M. Y. Rafii ◽

M. A. Latif ◽

Siti Zaharah Sakimin ◽

Ibrahim Wasiu Arolu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Diversity Index ◽

Gene Diversity ◽

Allelic Diversity ◽

Peninsular Malaysia ◽

Breeding Program ◽

Aromatic Rice ◽

Information Index ◽

Rice Germplasm

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon’s information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei’s gene diversity index of 0.36. The dendrogram based on UPGMA and Nei’s genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

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Genetic Diversity of Shanlan Upland Rice (Oryza sativa L.) and Association Analysis of SSR Markers Linked to Agronomic Traits

BioMed Research International ◽

10.1155/2021/7588652 ◽

2021 ◽

Vol 2021 ◽

pp. 1-11

Author(s):

Guofeng Yang ◽

Yong Yang ◽

Yali Guan ◽

Zhixia Xu ◽

Junyu Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Height ◽

Ssr Markers ◽

Agronomic Traits ◽

Upland Rice ◽

Diversity Index ◽

Oryza Sativa L ◽

Grain Number ◽

Rice Germplasm ◽

Panicle Number

Shanlan upland rice, a kind of unique rice germplasm in Hainan Island, was used to evaluate genetic diversity and association between SSR markers and agronomic traits. A total of 239 alleles were detected in 57 Hainan upland rice varieties using 35 SSR markers, and the number of alleles per locus was 2-19. The observed heterozygosity was 0.0655-0.3115. The Shannon diversity index was 0.1352-0.4827. The genetic similarity coefficient was 0.6736-0.9707, and 46 varieties were clustered into one group, indicating that the genetic base of the Shanlan upland rice germplasm was narrow. A total of 25 SSR markers significantly related to plant height, effective panicle number per plant, panicle length, total grain number, filled grain number, seed rating rate, and 1000-grain weight were obtained ( P < 0.01 ), with the percentage of the total variations explained ranging from 0.12% to 42.62%. RM208 explained 42.62% of the total variations in plant height of Shanlan upland rice. RM493 was significantly associated with 6 agronomic traits. We can speculate that RM208 may flank QTLs responsible for plant height and RM493 may flank QTLs playing a fundamental role in the intertwined regulatory network of agronomic traits of Shanlan upland rice.

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Assessment of the genetic diversity and population structure in temperate japonica rice germplasm used in breeding in Chile, with SSR markers

Chilean journal of agricultural research ◽

10.4067/s0718-58392017000100002 ◽

2017 ◽

Vol 77 (1) ◽

pp. 15-26 ◽

Cited By ~ 6

Author(s):

Viviana Becerra ◽

Mario Paredes ◽

Marcio E Ferreira ◽

Eduardo Gutierrez ◽

Lucy M Diaz

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Japonica Rice ◽

Temperate Japonica ◽

Rice Germplasm

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citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement

Genes ◽

10.3390/genes11121486 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1486

Author(s):

Naveen Duhan ◽

Manish Meshram ◽

Cristian D. Loaiza ◽

Rakesh Kaundal

Keyword(s):

Ssr Markers ◽

Molecular Breeding ◽

Crop Improvement ◽

Variety Identification ◽

Germplasm Characterization ◽

Citrus Species ◽

Genome Wide ◽

Genomic Regions ◽

Chromosome Scaffold ◽

Simple Sequence

Microsatellites or simple sequence repeats (SSRs) are popular co-dominant markers that play an important role in crop improvement. To enhance genomic resources in general horticulture, we identified SSRs in the genomes of eight citrus species and characterized their frequency and distribution in different genomic regions. Citrus is the world’s most widely cultivated fruit crop. We have implemented a microsatellite database, citSATdb, having the highest number (~1,296,500) of putative SSR markers from the genus Citrus, represented by eight species. The database is based on a three-tier approach using MySQL, PHP, and Apache. The markers can be searched using multiple search parameters including chromosome/scaffold number(s), motif types, repeat nucleotides (1–6), SSR length, patterns of repeat motifs and chromosome/scaffold location. The cross-species transferability of selected markers can be checked using e-PCR. Further, the markers can be visualized using the Jbrowse feature. These markers can be used for distinctness, uniformity, and stability (DUS) tests of variety identification, marker-assisted selection (MAS), gene discovery, QTL mapping, and germplasm characterization. citSATdb represents a comprehensive source of markers for developing/implementing new approaches for molecular breeding, required to enhance Citrus productivity. The potential polymorphic SSR markers identified by cross-species transferability could be used for genetic diversity and population distinction in other species.

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