Development of EST SSRs in Finger Millet (Eleusine coracana ssp coracana) and their Transferability to Pearl Millet (Pennisetum glaucum)

Arya, Lalit; Verma, Manjusha; Gupta, Veena; Karihaloo, J. L.

doi:10.1007/bf03263303

Cited by 38 publications

(13 citation statements)

References 11 publications

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“…Very few reports exist on the use of molecular markers for studying genetic diversity in finger millet, although the development and use of molecular markers in genomic studies of finger millet started a decade ago. Arya et al (2009) developed 31 expressed sequence tag simple sequence repeats (EST-SSRs), out of which 17 were amplified and nine were found to be polymorphic between 11 elite germplasm accessions of finger millet of Indian and African origin. Reddy et al (2012) identified 132 EST-based SSRs and developed 30 SSR primers for assessing genetic diversity in 15 finger millet accessions.…”

Section: Molecular Markers Genetic Diversity and Phylogenetic Studimentioning

confidence: 99%

Healthy and Resilient Cereals and Pseudo-Cereals for Marginal Agriculture: Molecular Advances for Improving Nutrient Bioavailability

et al. 2020

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With the ever-increasing world population, an extra 1.5 billion mouths need to be fed by 2050 with continuously dwindling arable land. Hence, it is imperative that extra food come from the marginal lands that are expected to be unsuitable for growing major staple crops under the adverse climate change scenario. Crop diversity provides right alternatives for marginal environments to improve food, feed, and nutritional security. Well-adapted and climate-resilient crops will be the best fit for such a scenario to produce seed and biomass. The minor millets are known for their high nutritional profile and better resilience for several abiotic stresses that make them the suitable crops for arid and salt-affected soils and poor-quality waters. Finger millet (Eleucine coracana) and foxtail millet (Setaria italica), also considered as orphan crops, are highly tolerant grass crop species that grow well in marginal and degraded lands of Africa and Asia with better nutritional profile. Another category of grains, called pseudo-cereals, is considered as rich foods because of their protein quality and content, high mineral content, and healthy and balance food quality. Quinoa (Chenopodium quinoa), amaranth (Amaranthus sp.), and buckwheat (Fagopyrum esculentum) fall under this category. Nevertheless, both minor millets and pseudo-cereals are morphologically different, although similar for micronutrient bioavailability, and their grains are gluten-free. The cultivation of these millets can make dry lands productive and ensure future food as well as nutritional security. Although the natural nutrient profile of these crop plant species is remarkably good, little development has occurred in advances in molecular genetics and breeding efforts to improve the bioavailability of nutrients. Recent advances in NGS have enabled the genome and transcriptome sequencing of these millets and pseudo-cereals for the faster development of molecular markers and application in molecular breeding. Genomic information on finger millet (1,196 Mb with 85,243 genes); S. italica, a model small millet (well-annotated draft genome of 420 Mb with 38,801 protein-coding genes); amaranth (466 Mb genome and 23,059 protein-coding genes); buckwheat (genome size of 1.12 Gb with 35,816 annotated genes); and quinoa (genome size of 1.5 Gb containing 54,438 protein-coding genes) could pave the way for the genetic improvement of these grains. These genomic resources are an important first step toward genetic improvement of these crops. This

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Section: Molecular Markers Genetic Diversity and Phylogenetic Studimentioning

confidence: 99%

Healthy and Resilient Cereals and Pseudo-Cereals for Marginal Agriculture: Molecular Advances for Improving Nutrient Bioavailability

et al. 2020

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“…Putative function for the majority of such markers can be deduced by database searches and other in silico approaches. EST-SSR markers are also expected to possess high inter-specific transferability as they belong to relatively conserved genic regions within the genome (Arya et al, 2009). Although, SSRs from EST sequences are very convenient for their ready use in diversity studies, limited availability of EST sequences (1956) so far at NCBI (Gene-bank) database for finger millet has limited the utilization of EST SSRs in finger millet.…”

Section: Molecular Markers For Assessing Genetic Diversity Species Rmentioning

confidence: 99%

“…Although, SSRs from EST sequences are very convenient for their ready use in diversity studies, limited availability of EST sequences (1956) so far at NCBI (Gene-bank) database for finger millet has limited the utilization of EST SSRs in finger millet. Characterization of 11 elite germplasm lines of finger millet of Indian and African origin using 31 SSRs from 1740 ESTs (based on di, tri, tetra and penta-nucleotide repeat sequences) gave an amplification product for 17 primer pairs, of which nine were found polymorphic with two alleles per locus (Arya et al, 2009). Similarly, Reddy et al (2012) mined 132 SSRs and designed 30 SSRs having base length of 20 or more for genetic diversity analysis of 15 finger millet accessions.…”

Section: Molecular Markers For Assessing Genetic Diversity Species Rmentioning

confidence: 99%

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics—An Important Nutri-Cereal of Future

et al. 2016

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The rapid strides in molecular marker technologies followed by genomics, and next generation sequencing advancements in three major crops (rice, maize and wheat) of the world have given opportunities for their use in the orphan, but highly valuable future crops, including finger millet [Eleusine coracana (L.) Gaertn.]. Finger millet has many special agronomic and nutritional characteristics, which make it an indispensable crop in arid, semi-arid, hilly and tribal areas of India and Africa. The crop has proven its adaptability in harsh conditions and has shown resilience to climate change. The adaptability traits of finger millet have shown the advantage over major cereal grains under stress conditions, revealing it as a storehouse of important genomic resources for crop improvement. Although new technologies for genomic studies are now available, progress in identifying and tapping these important alleles or genes is lacking. RAPDs were the default choice for genetic diversity studies in the crop until the last decade, but the subsequent development of SSRs and comparative genomics paved the way for the marker assisted selection in finger millet. Resistance gene homologs from NBS-LRR region of finger millet for blast and sequence variants for nutritional traits from other cereals have been developed and used invariably. Population structure analysis studies exhibit 2–4 sub-populations in the finger millet gene pool with separate grouping of Indian and exotic genotypes. Recently, the omics technologies have been efficiently applied to understand the nutritional variation, drought tolerance and gene mining. Progress has also occurred with respect to transgenics development. This review presents the current biotechnological advancements along with research gaps and future perspective of genomic research in finger millet.

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“…Similarly, more than 5,000 intron-length polymorphic markers were mined from the foxtail millet genome and mapped onto nine chromosomes to show their utilization in genotyping, phylogenetics, and comparative mapping in other millets and bio-energy grasses . The cross-species leveraging of molecular markers, like expressed sequence tag (EST)-SSR, was substantive to understand genetic relationships, marker-assisted selection (MAS), and comparative genomics in foxtail millet and other small millets Arya et al, 2009;Reddy et al, 2012;Kumari et al, 2013). Associations of gene-specific molecular markers were found related to a variety of traits in finger millet and foxtail millet.…”

Section: A Molecular Marker Resources and Genetic Mapsmentioning

confidence: 97%

Genetic and Genomic Resources of Small Millets

Saha

Gowda²,

Arya

et al. 2016

Critical Reviews in Plant Sciences

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Small millets are very promising agricultural entity to ensure global food security. They gained remarkable importance in agriculture due to their resilience to climatic changes and increasing demand for nutritious food and feed. The genetic variability in the core and mini-core germplasm of small millets was characterized for nutritional composition and capacity to tolerate abiotic stresses that can be infused in breeding programs. Other than the foxtail millet, availability of genomic information in small millets is far below the mark for use in marker-assisted breeding and other genetic improvement programs. The genome sequence of foxtail millet has recently triggered a plethora of post-genomic analysis and envisaged foxtail millet as a model organism for the C 4 grasses and bioenergy research. Recent developments in the next-generation sequencing technologies enabled us, with the simultaneous discovery of high-throughput markers and multiplexed genotyping of germplasm, to speedup markerassisted breeding. In this context, an in-depth analysis of the wealth of diverse germplasm resources and future perspectives of integrating genomics in genome-wide marker-trait association and breeding in small millets is worthy. ABBREVIATIONS cDNA D complementary DNA cM D centimorgan DREB D dehydration response element binding FAO D Food and Agricultural Organization ICAR D Indian Council of Agricultural Research ICRISAT D International Crops Research Institute for the Semi-Arid Tropics Mb D mega basepairs Mha D million hectares Mt D million tonnes Mya D million years ago NARS D National Agricultural Research System NCBI D National Center for Biotechnology Information NGS D next-generation sequencing PCR D polymerase chain reaction PGR D plant genetic resources SNP D single nucleotide polymorphism SSR D simple sequence repeat QTLs D quantitative trait loci

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Development of EST SSRs in Finger Millet (Eleusine coracana ssp coracana) and their Transferability to Pearl Millet (Pennisetum glaucum)

Cited by 38 publications

References 11 publications

Healthy and Resilient Cereals and Pseudo-Cereals for Marginal Agriculture: Molecular Advances for Improving Nutrient Bioavailability

Healthy and Resilient Cereals and Pseudo-Cereals for Marginal Agriculture: Molecular Advances for Improving Nutrient Bioavailability

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics—An Important Nutri-Cereal of Future

Genetic and Genomic Resources of Small Millets

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