Using molecular markers to assess the genetic diversity and population structure of finger millet (Eleusine coracana (L.) Gaertn.) from various geographical regions

Ramakrishnan, Muthusamy; Ceasar, S. Antony; Duraipandiyan, V.; Al-Dhabi, N. A.; Ignacimuthu, S.

doi:10.1007/s10722-015-0255-1

Cited by 56 publications

(24 citation statements)

References 72 publications

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“…et al (2014) used more accessions (190) than the current study but reported less polymorphism. Consistent with studies in other crops, SSR markers used in the current and previous studies (Dida et al 2008;Arya et al 2013) gave higher PIC values than other genetic diversity studies in finger millet with other markers such as ISSRs (Gupta et al 2010) and RAPDs (Das and Misra 2010;Bezawuletaw 2011;Ramakrishnan et al 2015). Although SNP markers have also been shown to be informative in other polyploid cereal crops such as wheat (Wang et al 2014), there are currently no known SNP assays developed for finger millet.…”

Section: Discussionsupporting

confidence: 84%

“…The weighted neighbour-joining tree constructed from pairwise genetic distances in the current study revealed that the clustering of African accessions was not entirely based on their geographical origin, confirming earlier reports for cultivated finger millet (Babu et al 2007;Dida et al 2008;Bezawuletaw 2011;Nethra et al 2014;Manyasa et al 2015). Previous studies that included both Asian and African finger millet collections revealed a distinct clustering pattern between Asian and African collections but not within each collection (Dida et al 2008;Arya et al 2013;Ramakrishnan et al 2015). The lower levels of geographical clustering within African collections could be attributed to cross-boundary farmer-tofarmer seed exchange, inter-population seed dispersal, migration and gene flow.…”

Section: Discussionmentioning

confidence: 86%

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Genetic diversity and association mapping of Ethiopian and exotic finger millet accessions

Lule¹,

Villiers²,

Fetene³

et al. 2018

Crop Pasture Sci.

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Combining morphological and molecular data to identify genetic variation and marker–trait association is one of the most important prerequisites for genomics-assisted selection in crop improvement. To this end, a total of 138 finger millet (Eleusine coracana subsp. coracana) accessions including five improved varieties were evaluated to assess the genetic variation and population structure and undertake association mapping. These accessions were basically collected from Ethiopia (96), Eritrea (8), Kenya (7), Zambia (9) and Zimbabwe (13). Finger millet accessions were evaluated in the field for 10 important agronomic traits and also characterised using a set of 20 microsatellite markers. Mean polymorphism information content of 0.61 was observed from a total of 222 alleles with an average of 11.1 alleles per microsatellite locus. About 61% of alleles detected were rare (<5%) and specific allele amplification was observed in 34 accessions. Both weighted neighbour-joining based clustering using molecular data and hierarchical clustering using phenotypic trait data grouped the 138 accessions into four major clusters that were not entirely based on their geographical origins. Genome-wide association studies depicted 16 significant (P < 0.01) associations between 13 microsatellite markers and six agronomic traits. Our results reveal a unique abundance of rare alleles in finger millet and highlight the need for more careful selection of genome-wide association studies in the future in order to capture the contribution of rare alleles to important agronomic traits.

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Section: Discussionsupporting

confidence: 84%

Section: Discussionmentioning

confidence: 86%

Genetic diversity and association mapping of Ethiopian and exotic finger millet accessions

Lule¹,

Villiers²,

Fetene³

et al. 2018

Crop Pasture Sci.

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“…This study found high percentage of polymorphism (77.78%) using six ISSR primers with inclusion of large number of finger millet accessions from diverse ecological condition and large geographical range such as Ethiopia, Zimbabwe and India. Similarly, Ramakrishnan et al (2016) reported 76.48% polymorphism on 128 genotypes using RAPD marker, Babu et al (2007) reported 91% polymorphism in 32 genotypes using RAPD marker; Bezaweletaw (2011) reported 72.35% percentage of polymorphism on 66 genotypes of finger millet from Ethiopia and Eritrea, and Fakrudin et al (2004) reported 85.82% percentage of polymorphism on 32 germplasms from Indian, while Panwar et al (2010) reported 56.17% polymorphisms in 83 genotypes using RAPD marker, Babu et al (2014) reported only 46% polymorphism in 190 genotypes of finger millet using SSR makers; Salimath et al (1995) reported 26% percentage of polymorphism on 17 genotypes of finger millet from Africa, Asia and Brazil. It may be because finger millet is a highly self-pollinated crop which resulted in low level of polymorphism by SSR marker analysis (Dida et al, 2007).…”

Section: Polymorphism and Genetic Diversitymentioning

confidence: 98%

Genetic diversity and population structure of Ethiopian finger millet (Eleusine coracana (L.) Gaertn) genotypes using inter simple sequence repeat (ISSR) markers

Brhane¹,

Haileselassie²,

Tesfaye³

2017

Afr. J. Biotechnol.

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Eleusine coracana is an annual allotetraploid (2n=4x=36) that belongs to grass family, Poaceae. This research aimed to investigate level of genetic diversity of 80 accessions using ISSR markers. DNA was extracted from a bulk of three plants per accession using a modified CTAB method. Six ISSR primers amplified a total of 45 clear and reproducible bands. The total genetic diversity (H) and Shannon's diversity information index (I) for the entire populations was 0.28 and 0.41, respectively. Analysis of molecular variance in both grouping and without grouping revealed larger genetic diversity within the populations (58.54%) than among populations (41.45%). Of the total genetic diversity, 5.88% was attributed to populations within groups, 38.33% was attributed to among groups and 55.79% was attributed to differences within populations. Both unweighted pair-group method with arithmetic average phenograms and a neighbor joining trees were constructed for the individuals and populations using Jaccard's similarity coefficient. Most individuals from all populations tended to form their own cluster, while only few of the individuals were distributed all over the tree. Generally, the result of the present study confirmed the presence of genetically diversified accessions that can be used to improve the productivity, collection, conservation and sustainable use.Key words: Eleusine coracana, gene flow, genetic diversity, inter simple sequence repeat (ISSR) marker, unweighted pair group method with arithmetic mean (UPGMA). INTRODUCTIONEleusine coracana, commonly called finger millet, is an annual allotetraploid (2n=4x=36; genome constitution AABB) cultivated plant that belongs to the grass family Poaceae, subfamily Chloridoideae. There are about nine species under the genus, Eleusine Gaertn. Two species, Eleusine indica and Eleusine floccifolia, are believed to be the genome donors to the cultivated species, E. coracana (Bisht and Mukai, 2001).It is extensively cultivated in the tropical and subtropical regions of Africa and India and is known to save *Corresponding author. E-mail: haftom12388@yahoo.com. the lives of poor farmers from starvation at times of extreme drought (Kotschi, 2006). It is adapted to a wide range of environments and grown mainly by subsistence farmers. Finger millet serves as a food security crop because of its high nutritional value, excellent storage qualities and its importance as a low input crop (Dida et al., 2007). Ethiopia is one of the major producers of finger millet in addition to Uganda, India, Nepal and China and it is also native to the highlands of the country. Finger millet plays an important role in both the dietary needs and incomes of many rural households like other African countries due to its richness in fiber, iron and calcium (Babu et al., 2007).Assessment of genetic diversity on the basis of morphological traits is not very reliable, as it may be influenced by the environment, and the number of traits with known inheritance is small. Molecular markers have the distinct advantages...

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“…This could be attributed to narrow genetic pool of cultivated finger millet. However, studies using RAPD markers for genetic diversity observed higher polymorphism ranging from 35 to 100% (Fakrudin et al, 2004; Kalyana Babu et al, 2007; Das and Misra, 2010; Kumari and Pande, 2010; Panwar et al, 2010a; Singh and Kumar, 2010; Ramakrishnan et al, 2015). In all these studies, phenograms based on the RAPD markers data could clearly distinguish the genotypes from different geographical regions as separate clusters.…”

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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Using molecular markers to assess the genetic diversity and population structure of finger millet (Eleusine coracana (L.) Gaertn.) from various geographical regions

Cited by 56 publications

References 72 publications

Genetic diversity and association mapping of Ethiopian and exotic finger millet accessions

Genetic diversity and association mapping of Ethiopian and exotic finger millet accessions

Genetic diversity and population structure of Ethiopian finger millet (Eleusine coracana (L.) Gaertn) genotypes using inter simple sequence repeat (ISSR) markers

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

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