Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis

Development of simple sequence repeat markers for sugarcane from data mining of expressed sequence tags

Sugarcane (Saccharum spp. hybrids) is a worldwide acclaimed important agricultural crop used primarily for sugar production and biofuel. Sugarcane's genetic complexity, aneuploidy, and extreme heterozygosity make it a challenging crop in developing improved varieties. The molecular breeding programs promise to develop nutritionally improved varieties for both direct consumption and commercial application. Therefore, to address these challenges, the development of simple sequence repeats (SSRs) has been proven to be a powerful molecular tool in sugarcane. This study involved the collection of 285216 expressed sequence tags (ESTs) from sugarcane, resulting in 23666 unigenes, including 4547 contigs. Our analysis identified 4120 unigenes containing a total of 4960 SSRs, with the most abundant repeat types being monomeric (44.33%), dimeric (13.10%), and trimeric (39.68%). We further chose 173 primers to analyze the banding pattern in 10 sugarcane accessions by PAGE analysis. Additionally, functional annotation analysis showed that 71.07%, 53.6%, and 10.3% unigenes were annotated by Uniport, GO, and KEGG, respectively. GO annotations and KEGG pathways were distributed across three functional categories: molecular (46.46%), cellular (33.94%), and biological pathways (19.6%). The cluster analysis indicated the formation of four distinct clusters among selected sugarcane accessions, with maximum genetic distance observed among the varieties. We believe that these EST-SSR markers will serve as valuable references for future genetic characterization, species identification, and breeding efforts in sugarcane.

Exploring the genetic makeup and population structure among Capsicum accessions for crop improvement and breeding curriculum insights

Background

Capsicum or chilli is an important crop in India which exhibits immense structural and genetic variations reflecting their intra- and inter-specific relationships. The aim of this study was to establish relationships amongst 54 Capsicum accessions through analysis of genetic and population structure using ISSR markers.

Results

Out of 19, successful DNA amplifications were shown by 7 ISSR primers and a total of 80 bands were identified ranging between 8 and 14 with an average of 11.43 bands/primer. A significant degree of polymorphic information content (PIC), discriminating power (DP), resolving power (RP), effective multiplex ratio (EMR), and marker index (MI) were identified as 0.39, 0.70, 6.40, 5.88, and 2.30, respectively, using ISSR markers in chillies. The cross-transferability ranged from 8.0 to 72.15% with an average of 52.63% among chillies. Amongst genetic information, grand mean values were 0.264, 0.180, 0.376, 0.296, and 0.180, which correspond to Shannon’s information index (I), expected heterozygosity (He), Nei’s gene diversity, total diversity among species (Ht), diversity within species (Hs), respectively. Further, the coefficients of gene differentiation (Gst) and gene flow (Nm) were 0.393 and 0.773, representing higher genetic variation among the population which was confirmed by analysis of molecular variance (AMOVA).

Conclusion

ISSR markers represented a potent system for the estimation of relationships or variation studies and generated information useful for planning crop management and improvement strategies in chilli breeding.

Protocol development for somatic embryogenesis, SSR markers and genetic modification of Stipagrostis pennata (Trin.) De Winter

BACKGROUND

Stipagrostis pennata (Trin.) De Winter is an important species for fixing sand in shifting and semi-fixed sandy lands, for grazing, and potentially as a source of lignocellulose fibres for pulp and paper industry. The seeds have low viability, which limits uses for revegetation. Somatic embryogenesis offers an alternative method for obtaining large numbers of plants from limited seed sources.

RESULTS

A protocol for plant regeneration from somatic embryos of S. pennata was developed. Somatic embryogenesis was induced on Murashige & Skoog (MS) medium supplemented with 3 mg·L-1 2,4-D subsequently shoots were induced on MS medium and supplemented with 5 mg·L-1 zeatin riboside. The highest shoots induction was obtained when embryogenic callus derived from mature embryos (96%) in combination with MS filter-sterilized medium was used from Khuzestan location. The genetic stability of regenerated plants was analysed using ten simple sequence repeats (SSR) markers from S. pennata which showed no somaclonal variation in regenerated plants from somatic embryos of S. pennata. The regenerated plants of S. pennata showed genetic stability without any somaclonal variation for the four pairs of primers that gave the expected amplicon sizes. This data seems very reliable as three of the PCR products belonged to the coding region of the genome. Furthermore, stable expression of GUS was obtained after Agrobacterium-mediated transformation using a super binary vector carried by a bacterial strain LBA4404.

CONCLUSION

To our knowledge, the current work is the first attempt to develop an in vitro protocol for somatic embryogenesis including the SSR marker analyses of regenerated plants, and Agrobacterium-mediated transformation of S. pennata that can be used for its large-scale production for commercial purposes.

Development of EST-SSR markers for Pongamia pinnata by transcriptome database mining: cross-species amplification and genetic diversity

EST-SSR markers were developed from Pongamia pinnata transcriptome libraries. We have successfully utilised EST-SSRs to study the genetic diversity of Indian P. pinnata germplasms and transferability study on legume plants. P. pinnata is a non-edible oil, seed-bearing leguminous tree well known for its multipurpose benefits and acts as a potential source for medicine and biodiesel preparation. Moreover, the plant is not grazable by animal and wildly grown in different agro climatic condition of India. Recently, it is much used in reforestation and rehabilitation of marginal and coal mined land in different part of India. Due to increasing demand for cultivation, understanding of the genetic diversity is important parameter for further breeding and cultivation program. In this investigation, an attempt has been undertaken to develop novel EST-SSR markers by analyzing the assembled transcriptome from previously published Illumina libraries of P. pinnata, which is cross transferrable to legume plants. Twenty EST-SSR markers were developed from oil yielding and secondary metabolite biosynthesis genes. To our knowledge, this is the first EST-SSR marker based genetic diversity study on Indian P. pinnata germplasms. The genetic diversity parameter analysis of P. pinnata showed that the Gangetic plain and Eastern India are highly diverse compared to the Central Deccan and Western germplasms. The lowest genetic diversity in the Western region may be due to the pressure of lower precipitation, high-temperature stress and reduced groundwater availability. Nevertheless, the highest genetic diversity of Gangetic plain and Eastern India may be due to the higher groundwater availability, high precipitation, higher temperature fluctuations and growing by the side of glacier-fed river water. Thus, our study shows the evidence of natural selection on the genetic diversity of P. pinnata germplasms of the Indian subcontinent.

Screening of EMS-Induced Drought-Tolerant Sugarcane Mutants Employing Physiological, Molecular and Enzymatic Approaches

Drought stress is one of the major agronomic concerns that lead towards a sharp decline in sugarcane yield. An urgent demand to overcome drought is critical to ensure sugarcane production. Mutation breeding is one of the promising tools available to produce stress-resistant plants, with the induction of new alleles due to point mutation within existing sugarcane germplasm. The current study was directed to chemically mutagenize the calli of two sugarcane cultivars (ROC22 and FN39) via 0.1% EMS, with focus on inducing mutations in their genome. The 1644 regenerated plants of ROC22 and 1398 of FN39 were exposed to 28% PEG-6000 stimulated osmotic stress. Eighteen plants of ROC22 and 2 plants of FN39, that survived after in vitro osmotic stress treatment, were then subjected to preliminary greenhouse pot trials to confirm drought tolerance by analyzing them using various physiological parameters, including photosystem II (PSII) photochemical efficiency (Fv/Fm), leaf chlorophyll content, and photosynthetic rate. The genetic diversity among drought-resistant mutant lines was further assessed by 15 pairs of simple sequence repeat (SSR) markers amplification and CEL (Celery) I endonuclease digestion, to investigate the mutated sites. Mutant lines of ROC22 (i.e., MR22-15 and MR22-20) were found to be promising for future drought resistance breeding, due to better physiological adaptation under drought stress.

Molecular diversity analysis, drought related marker-traits association mapping and discovery of excellent alleles for 100-day old plants by EST-SSRs in cassava germplasms (Manihot esculenta Cranz)

Cassava is the third largest food crop of the world and has strong ability of drought tolerance. In order to evaluate the molecular diversity and to discover novel alleles for drought tolerance in cassava germplasms, we examined a total of 107 abiotic stress related expressed sequence tags-simple sequence repeat (EST-SSR) markers in 134 cassava genotypes coming from planting regions worldwide and performed drought related marker-traits association mapping. As results, we successfully amplified 98 of 107 markers in 97 polymorphic loci and 279 alleles, with 2.87 alleles per locus, gene diversity of 0.48 and polymorphic information content (PIC) of 0.41 on average. The genetic coefficient between every two lines was 0.37 on average, ranging from 0.21 to 0.82. According to our population structure analysis, these samples could be divided into three sub-populations showing obvious gene flow between them. We also performed water stress experiments using 100-day old cassava plants in two years and calculated the drought tolerance coefficients (DTCs) and used them as phenotypes for marker-trait association mapping. We found that 53 markers were significantly associated with these drought-related traits, with a contribution rate for trait variation of 8.60% on average, ranging between 2.66 and 28.09%. Twenty-four of these 53 associated genes showed differential transcription or protein levels which were confirmed by qRT-PCR under drought stress when compared to the control conditions in cassava. Twelve of twenty-four genes were the same differential expression patterns in omics data and results of qRT-PCR. Out of 33 marker-traits combinations on 24 loci, 34 were positive and 53 negative alleles according to their phenotypic effects and we also obtained the typical materials which carried these elite alleles. We also found 23 positive average allele effects while 10 loci were negative according to their allele effects (AAEs). Our results on molecular diversity, locus association and differential expression under drought can prove beneficial to select excellent materials through marker assisted selection and for functional genes research in the future.

Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae)

The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized. The nuclear content of DNA for all analyzed Theobroma species was 1C = ~ 0.46 pg. These species presented 2n = 20 with small chromosomes and only one pair of terminal heterochromatic bands positively stained (CMA⁺/DAPI⁻ bands). The small size of Theobroma ssp. genomes was equivalent to other Byttnerioideae species, suggesting that the basal lineage of Malvaceae have smaller genomes and that there was an expansion of 2C values in the more specialized family clades. A set of 20 EST-SSR primers were characterized for related species of Theobroma, in which 12 loci were polymorphic. The polymorphism information content (PIC) ranged from 0.23 to 0.65, indicating a high level of information per locus. Combined results of flow cytometry, cytogenetic data and EST-SSRs markers will contribute to better describe the species and infer about the evolutionary relationships among Theobroma species. In addition, the importance of a core collection for conservation purposes is highlighted.