Tracing QTLs for Leaf Blast Resistance and Agronomic Performance of Finger Millet (Eleusine coracana (L.) Gaertn.) Genotypes through Association Mapping and in silico Comparative Genomics Analyses.

M Ramakrishnan,V Duraipandiyan,S Ignacimuthu,S Antony Ceasar,N A Al-Dhabi,Krishnan Kalpana,K K Vinod,Swarup Kumar Parida

doi:10.1371/journal.pone.0159264

Abstract

Finger millet is one of the small millets with high nutritive value. This crop is vulnerable to blast disease caused by Pyricularia grisea, which occurs annually during rainy and winter seasons. Leaf blast occurs at early crop stage and is highly damaging. Mapping of resistance genes and other quantitative trait loci (QTLs) for agronomic performance can be of great use for improving finger millet genotypes. Evaluation of one hundred and twenty-eight finger millet genotypes in natural field conditions revealed that leaf blast caused severe setback on agronomic performance for susceptible genotypes, most significant traits being plant height and root length. Plant height was reduced under disease severity while root length was increased. Among the genotypes, IE4795 showed superior response in terms of both disease resistance and better agronomic performance. A total of seven unambiguous QTLs were found to be associated with various agronomic traits including leaf blast resistance by association mapping analysis. The markers, UGEP101 and UGEP95, were strongly associated with blast resistance. UGEP98 was associated with tiller number and UGEP9 was associated with root length and seed yield. Cross species validation of markers revealed that 12 candidate genes were associated with 8 QTLs in the genomes of grass species such as rice, foxtail millet, maize, Brachypodium stacei, B. distachyon, Panicum hallii and switchgrass. Several candidate genes were found proximal to orthologous sequences of the identified QTLs such as 1,4-β-glucanase for leaf blast resistance, cytokinin dehydrogenase (CKX) for tiller production, calmodulin (CaM) binding protein for seed yield and pectin methylesterase inhibitor (PMEI) for root growth and development. Most of these QTLs and their putatively associated candidate genes are reported for first time in finger millet. On validation, these novel QTLs may be utilized in future for marker assisted breeding for the development of fungal resistant and high yielding varieties of finger millet.

Highlights

Finger millet (Eleusine coracana (L.) Gaertn.) is one of the small millets grown in different parts of the world including India
The analysis revealed that only two traits such as plant height and root length were significantly associated with leaf blast incidence, wherein plant height had a negative influence on percent disease incidence (PDI) (-0.25) while the length of root had a significant positive influence on PDI (1.78)
Finger millet accessions in this study showed significant variation in resistance to leaf blast disease that had greatly altered their agronomic performance

Summary

Introduction

Finger millet (Eleusine coracana (L.) Gaertn.) is one of the small millets grown in different parts of the world including India. Known as ragi in India, this cereal occupies about 2.7 million hectares of cultivation worldwide especially in developing countries (Africa and Asia) with an annual production of 2.6 million tons with a contribution of about 10% of global millet production; 94% of the global finger millet production occurs in Africa and Asia [2]. This crop is highly vulnerable to leaf blast disease caused by Pyricularia grisea (teleomorph: Magnaporthe grisea) [3], and probably the only and most destructive disease occurring annually during rainy and winter seasons [2]. It is estimated that average yield loss due to blast diseases is around 28–36% each year in Asia [5] and in certain areas yield losses can go as high as 80–100% [6]

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