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

Abstract

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.

A review of the orphan small grain cereals improvement with a comprehensive plan for genomics‐assisted breeding of fonio millet in West Africa

“…The germplasms collected were characterized at both phenotypic and genotypic levels. At the phenotypic level, various agro morphological descriptors were used for evaluation of orphan small cereal accessions (Ben‐Zeev et al., 2018; Nyam et al., 2017; Patil et al., 2019) whereas at the genotypic level a variety of molecular markers were used for genetic diversity and population structure studies (Girma et al., 2018; Lule et al., 2018; Manimekalai et al., 2018; Olodo et al., 2018; Yadav et al., 2016). This shows the significant importance of these markers that provide useful tools for population and evolutionary genetics studies of orphan small millets.…”

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

“…Past DNA-based studies of finger millet genetic diversity have generally been limited in scope, involving < 150 accessions and/or < 100 polymorphic loci. These studies include those of Dida et al (2008), Arya et al (2013), Manyasa et al (2015), Ramakrishnan et al (2016), Babu et al (2018), Lule et al (2018) and Pandian et al (2018) who all applied simple sequence repeat (SSR) markers; and those of Gimode et al (2016) and Sood et al (2016) who used SSRs and SNPs.…”

Genetic and genomic resources for finger millet improvement: opportunities for advancing climate-smart agriculture

“…Linkage and association mapping are the two most common methods used for identifying QTL conditioning complex traits; through these methods genes/QTL have been identified in different plant species (Yang et al 2011;Zhang et al 2016;Lule et al 2018;Sharma et al 2018). Since the development of bi-parental mapping populations for small millets is a difficult, the classical linkage analysis of QTL for traits associated with climatic stresses is limited.…”