Genome-wide association mapping for seed protein content in finger millet (Eleusine coracana) global collection through genotyping by sequencing

Tiwari, Apoorv; Sharma, Divya; Sood, Salej; Jaiswal, J. P.; Pachauri, S. P.; Ramteke, Pramod W.; Kumar, Anil

doi:10.1016/j.jcs.2019.102888

Cited by 31 publications

(19 citation statements)

References 41 publications

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“…To supplement conventional breeding, shorten breeding cycles, and accelerate research activities, powerful tools, such as speed breeding protocols, which accelerate plant growth and development, may be explored in finger millet breeding strategies (Watson et al, 2018). Speed breeding technology is able to achieve up to six generations per year of barley (Hickey et al, 2017), wheat (Watson et al, 2018), and oats (González-Barrios et al, 2020), presenting a robust tool to reduce the long period of breeding cycles effectively. Several speed breeding protocols that utilize prolonged photoperiods and controlled temperatures to accelerate growth and development have been developed for the world's major cereals.…”

Section: Breeding Approaches For Improvement Of Disease-resistant Varmentioning

confidence: 99%

“…Although the genome sequence for finger millet has not been release so far, considerable gains of GBS have been achieved. For example, Tiwari et al (2020) discovered genes and QTLs governing seed protein content and related traits in finger millet using SNPs discovered via GBS technology. Likewise, GBS was used to identify genomic regions which govern grain nutritional traits in finger millet and generated 169,365 SNPs and three subpopulations ( Puranik et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Breeding Strategies and Challenges in the Improvement of Blast Disease Resistance in Finger Millet. A Current Review

Mbinda

Masaki

2021

Front. Plant Sci.

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Climate change has significantly altered the biodiversity of crop pests and pathogens, posing a major challenge to sustainable crop production. At the same time, with the increasing global population, there is growing pressure on plant breeders to secure the projected food demand by improving the prevailing yield of major food crops. Finger millet is an important cereal crop in southern Asia and eastern Africa, with excellent nutraceutical properties, long storage period, and a unique ability to grow under arid and semi-arid environmental conditions. Finger millet blast disease caused by the filamentous ascomycetous fungus Magnaporthe oryzae is the most devastating disease affecting the growth and yield of this crop in all its growing regions. The frequent breakdown of blast resistance because of the susceptibility to rapidly evolving virulent genes of the pathogen causes yield instability in all finger millet-growing areas. The deployment of novel and efficient strategies that provide dynamic and durable resistance against many biotypes of the pathogen and across a wide range of agro-ecological zones guarantees future sustainable production of finger millet. Here, we analyze the breeding strategies currently being used for improving resistance to disease and discuss potential future directions toward the development of new blast-resistant finger millet varieties, providing a comprehensive understanding of promising concepts for finger millet breeding. The review also includes empirical examples of how advanced molecular tools have been used in breeding durably blast-resistant cultivars. The techniques highlighted are cost-effective high-throughput methods that strongly reduce the generation cycle and accelerate both breeding and research programs, providing an alternative to conventional breeding methods for rapid introgression of disease resistance genes into favorable, susceptible cultivars. New information and knowledge gathered here will undoubtedly offer new insights into sustainable finger millet disease control and efficient optimization of the crop’s productivity.

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Section: Breeding Approaches For Improvement Of Disease-resistant Varmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Breeding Strategies and Challenges in the Improvement of Blast Disease Resistance in Finger Millet. A Current Review

Mbinda

Masaki

2021

Front. Plant Sci.

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“…Coexistence of competing species are limited by most of the resources and the consumption of most limited resource is at higher rate than the other species which can be explained by prevailing models (Tilman 1982). Strong support for the mechanism of coexistence among aquatic organisms has been proved by the studies but limited evidences are found in support of terrestrial plants (Dybzinski and Tilman 2007;Miller et al 2005;Schamp et al 2008).…”

Section: Co-existence Of Different Plants-microbes and Resource Partimentioning

confidence: 99%

Mainstreaming Barahnaja cultivation for food and nutritional security in the Himalayan region

et al. 2021

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Selective production of input intensive crops in the present scenario have resulted in productivity stagnation or even decline due to excessive usage of chemicals, affecting the farmers economically. Sustainable agriculture is the way to increase agricultural productivity and economic prosperity by protecting all natural resources. It maintains a balance of soil fertility with crop productivity and nutritional quality. The mixed cropping systems followed earlier in different regions according to their tradition, climatic zone, soil and water conditions were climate-smart approaches to sustainable food production based on practical experiences over the years of old generations. The life style changes, imbalance in farming system in last 70 years and demand for more food as well as declining land resources resulted in intensive agriculture. Besides, least returns and less demand of ethnic crops gave more preference to major staple food crops. Barahnaja is a traditional orphan crops based mixed cropping system practiced in Himalayan region due to its sustainability and assured crop harvest during erratic weather conditions. This traditional farming method is an exemplary scientific approach to derive innovations with respect to productivity, quality, plant soil interactions and organic agriculture. The main focus of the review is to substantiate the characteristics of the traditional mixed cropping system by describing the advantages of the system and opportunities for scientific innovation towards new knowledge and sustainability.

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“…However, again the accessions and/or molecular markers involved were generally limited to small numbers, and studies did not have available a finger millet genome assembly to map markers to chromosome positions. These studies include those of Dida et al (2021) who used a medium-sized panel of SNPs but only 52 East African accessions to search for blast disease resistance MTAs; Puranik et al (2020) who used a large panel of SNPs but assessed only 190 genotypes to search for grain nutrient-content-related MTAs; Sharma et al (2018) who applied a medium-sized panel of SNPs to only 113 accessions to search for MTAs in 14 agro-morphological traits; and Tiwari et al (2020) who, beginning with the same SNPs and germplasm panel of Sharma et al (2018), explored marker associations with grain protein content. Despite their limited scope, these previous studies indicated some MTAs.…”

Section: Characterization Of Finger Milletmentioning

confidence: 99%

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Bančič

Odeny

et al. 2021

Preprint

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Advances in sequencing technologies mean that insights into crop diversification aiding future breeding can now be explored in crops beyond major staples. For the first time, we use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the sub-genome level. A set of 8,778 SNPs and 13 agronomic traits characterizing a broad panel of 423 landrace accessions from Africa and Asia suggested the crop has undergone complex, context-specific diversification consistent with a long domestication history. Both Principal Component Analysis and Discriminant Analysis of Principal Components of SNPs indicated four groups of accessions that coincided with the principal geographic areas of finger millet cultivation. East Africa, the considered origin of the crop, appeared the least genetically diverse. A Principal Component Analysis of phenotypic data also indicated clear geographic differentiation, but different relationships among geographic areas than genomic data. Neighbour-joining trees of sub-genomes A and B showed different features which further supported the crop’s complex evolutionary history. Our genome-wide association study indicated only a small number of significant marker-trait associations. We applied then clustering to marker effects from a ridge regression model for each trait which revealed two clusters of different trait complexity, with days to flowering and threshing percentage among simple traits, and finger length and grain yield among more complex traits. Our study provides comprehensive new knowledge on the distribution of genomic and phenotypic variation in finger millet, supporting future breeding intra- and inter-regionally across its major cultivation range.Core ideas8,778 SNPs and 13 agronomic traits characterized a panel of 423 finger millet landraces.4 clusters of accessions coincided with major geographic areas of finger millet cultivation.A comparison of phenotypic and genomic data indicated a complex diversification history.This was confirmed by the analysis of allotetraploid finger millet’s separate sub-genomes.Comprehensive new knowledge for intra- and inter-regional breeding is provided.

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Genome-wide association mapping for seed protein content in finger millet (Eleusine coracana) global collection through genotyping by sequencing

Cited by 31 publications

References 41 publications

Breeding Strategies and Challenges in the Improvement of Blast Disease Resistance in Finger Millet. A Current Review

Breeding Strategies and Challenges in the Improvement of Blast Disease Resistance in Finger Millet. A Current Review

Mainstreaming Barahnaja cultivation for food and nutritional security in the Himalayan region

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

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