Response to early drought stress and identification of QTLs controlling biomass production under drought in pearl millet

Marilyne Debieu,Sixtine Passot,Daniel Foncéka,Yves Vigouroux,Laurent Laplaze,Prakash Gangashetty,Alexandre Grondin,Pascal Gantet,Laurent Cournac,Eyanawa Akata,Charles Tom Hash,Ndjido Ardo Kane,Vincent Vadez,Bassirou Sine

doi:10.1371/journal.pone.0201635

Abstract

Pearl millet plays a major role in food security in arid and semi-arid areas of Africa and India. However, it lags behind the other cereal crops in terms of genetic improvement. The recent sequencing of its genome opens the way to the use of modern genomic tools for breeding. Our study aimed at identifying genetic components involved in early drought stress tolerance as a first step toward the development of improved pearl millet varieties or hybrids. A panel of 188 inbred lines from West Africa was phenotyped under early drought stress and well-irrigated conditions. We found a strong impact of drought stress on yield components. This impact was variable between inbred lines. We then performed an association analysis with a total of 392,493 SNPs identified using Genotyping-by-Sequencing (GBS). Correcting for genetic relatedness, genome wide association study identified QTLs for biomass production in early drought stress conditions and for stay-green trait. In particular, genes involved in the sirohaem and wax biosynthesis pathways were found to co-locate with two of these QTLs. Our results might contribute to breed pearl millet lines with improved yield under drought stress.

Highlights

In early drought stress treatments, fraction of transpirable soil water (FTSW) was below 40% in 0–60 cm soil profiles at 40 days after sowing (DAS) in 2015 and at 49 days in 2016
In 2015, water remained limiting for plant growth (FTSW below 40%) along the soil profile (0–120 cm) until around 110 DAS, extending the water-limiting period to the reproductive stage
In 2016, irrigation of the field at 49 DAS allowed increase in FTSW to around 40% at 55 DAS between 60–120 cm, short periods of water limiting conditions appeared at reproductive stage

Summary

Introduction

Pearl millet is the staple crop of more than 90 million farmers. Grains are glutenfree and rich in proteins and essential micronutrients such as iron or zinc. It is consumed directly as couscous or porridge and used to make flour to produce flat bread or to be introduced in bread production to reduce the imports of wheat in some African countries. Pearl millet lags behind the other cereal crops in terms of genetic improvement and its average yields are still low. The recent sequencing of its genome [2] opens the way to tap on its large genetic diversity to breed varieties and hybrids adapted to current and predicted future climatic constraints [3]

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