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Recent Advances in the Marker-Assisted Selection for Drought Tolerance in Pearl Millet

Rachid Serraj1, C.T. Hash1, Rattan S. Yadav2 and Fran R. Bidinger1

1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh,
E-mails:, ,
Institute of Grassland & Environmental Research, Aberystwyth SY23 3EB, United Kingdom Email


Pearl millet [Pennisetum glaucum (L.) R. Br.] is the staple cereal of the hottest, driest areas of the tropics where drought stress is a regular occurrence, making stress tolerance an essential attribute of new cultivars. Current breeding research has mapped several quantitative trait loci (QTL) for grain and stover yield under terminal drought stress conditions, and has evaluated these as possible selection criteria for improved stress tolerance. Initial evaluations, which were based on hybrids made with topcross pollinators composed of lines selected directly from the mapping population, indicated an advantage to the QTL-based topcross hybrids under terminal stress, which seemed to be related to particular plant phenotype which was similar to that of the tolerant parent of the mapping population. Subsequent evaluations were based on hybrids of NILs of the susceptible parent of the mapping population, which were bred by marker-assisted backcrossing of the putative drought tolerant QTL into these lines. Several of these lines had a significant positive general combining ability for grain yield under terminal stress and out yielded the hybrids made on the original recurrent parent in both unrelieved terminal tress and in gradient stress evaluations.

Media summary

Marker-assisted breeding in pearl millet based on QTL mapping for yield under terminal drought and its evaluation as possible selection criteria for improved stress tolerance

Key words

Drought, Marker-assisted breeding, QTL mapping, near isogenic lines, Pennisetum glaucum


The general complexity of drought stress is aggravated in the semi-arid tropics by highly unpredictable rainfall, and by high temperatures, high levels of solar radiation, and low soil fertility. The resulting large variability in the nature and occurrence of drought stress and the insufficient understanding of its complexity have made it generally difficult to characterize the physiological traits required for improved crop performance under drought, consequently limiting the use of a trait-based approach in plant breeding to enhance crop drought tolerance. Pearl millet is generally known for its relative ability to withstand periods of water-limited conditions and still produce biomass and grain (Bidinger and Hash, 2003). Even for this crop, however, the constant challenge is to reduce yield gaps between research plots and farmers’ fields, to assure sustained food security for resource poor farmers. Specifically the task is two fold: (1) to identify plant responses to the patterns of stress with the greatest effect on crop yields, which will minimize yield loss, or plant traits which will allow some measure of continued plant function despite the stress and (2) to research ways of incorporating these responses/traits into new varieties to both increase their overall productivity under stress and reduce the spatial and temporal variance in productivity.

The most relevant way of addressing this challenge is through a holistic approach integrating physiological dissection of selected resistance traits and the application of molecular genetic tools, with agronomic practices that lead to better utilization of soil moisture and matching crop genotypes with the production environment. This paper summarizes the recent progress made at ICRISAT in using new molecular tools to breed more drought tolerant varieties.

Characterization and molecular mapping of terminal drought tolerance

Genetic improvement of stress tolerance in pearl millet has concentrated on the flowering and grain filling stages as stress in this period has the greatest effect on grain yield (Mahalakshmi et. al. 1987). Statistical procedures have been developed to partition crop yield under stress into effects of stress escape, yield potential and stress response (Bidinger et al, 1987), and emphasis has been on identification and selection for traits related to stress tolerance rather than yield. A series of empirical selection experiments using panicle harvest index as a tolerance criterion resulted in small (5%) but significant gains in yield in selected materials under terminal stress (Bidinger et al, 2000; unpublished data).

Emphasis in more recent research has been on the identification and evaluation of QTL associated with both grain yield and with stress tolerance under terminal stress. Two mapping populations based on hybrid parents with known response to stress were created, genotyped and phenotyped under managed field stress conditions (Yadav et al., 2002, 2004). Both exercises identified a major, consistent QTL for grain yield, or the ability to maintain grain yield, under stress on linkage group 2 (LG 2), plus a number of minor QTL for both yield and yield components which were identified in some but not all phenotyping environments. In most, but not all, cases the drought tolerant parent contributed the positive allele. Analysis of co-mapping of QTL for individual traits and grain yield under stress, suggested a linkage between the ability to maintain grain yield under stress and the ability to maintain both panicle harvest index (primarily grain filling) and harvest index under terminal stress, as well as confirming the benefits of drought escape achieved through early flowering (Yadav et al., 2002,2004). Current emphasis is on the evaluation of effects of the identified QTL in the improvement of drought tolerance. Results from the first mapping population are described below.

Evaluation of drought tolerance QTL effects on phenotype

A simple initial evaluation of the putative drought tolerance QTL on LG 2 as a selection criterion was made by comparing hybrids made with topcross pollinators bred from progenies selected from the original mapping population for presence of the tolerant allele at the target QTL vs. for field performance in the phenotyping environments (Bidinger et al., submitted). A set of 36 topcross hybrids was evaluated in 21 field environments, which included both non-stressed and drought stressed treatments during the flowering and grain filling stages. The QTL-based hybrids were significantly, but modestly, higher yielding in a series of both absolute and partial terminal stress environments, but at the cost of a lower yield in the non-stressed evaluation environments. This particular pattern of adaptation in the QTL-based hybrids was consistent with their general phenotype – earlier flowering, limited effective basal tillering, lower biomass and a higher harvest index – which resembled the phenotype of the drought tolerant parent of the original mapping population, and which appeared to provide advantages under a post-flowering stress. The results thus confirmed the effectiveness of the putative drought tolerance QTL on LG 2, but suggested that it may enhance drought tolerance by favoring a phenotype with adaptation to terminal stress, rather than by improving drought tolerance at a more basic physiological level, at least when used as a direct selection criterion.

Field Evaluation of Drought NIL-QTLs

A more rigorous evaluation of the putative drought tolerance QTL is currently underway, using new near-isogenic versions of H 77/833-2, into which various putative drought tolerance QTL segments have been introgressed from donor parent PRLT 2/89-33 by marker-assisted backcrossing. BC4F3 progenies from selected BC4F2 plants homozygous for various portions of the LG2 target region were crossed to each of five different seed parents, and the resulting hybrids were evaluated under a range of moisture regimes (non-stressed control, early-onset, medium-onset and late-onset terminal drought stress). The hybrids exhibited a large variation in yield component expression and yield response to the moisture regimes, but there was a consistent yield advantage in hybrids carrying alleles from the drought tolerant donor parent PRLT 2/89-33 in the vicinity of the target QTL. Several of the introgression lines had a significant, positive general combining ability (across all testcrosses) for grain yield under terminal stress, which was associated with a higher panicle harvest index. Interestingly this superior grain yield performance of the introgression line hybrids was often accompanied by increased biomass yields and reduced grain harvest indices instead of the reduced biomass yield and increased grain harvest index that contribute to the higher grain yield potential and superior terminal drought tolerance for grain yield of hybrids of the donor parent. Thus these hybrids have potentially greater value for dual-purpose use (grain and stover), under water-limited conditions, than hybrids of either the donor parent or recurrent parent used in breeding their pollinators.

A line-source, gradient stress experiment was conducted to further compare the performance of selected NIL from general combining ability trial. These included test crosses (on four seed parents) of the two pollinators with the highest GCA for yield under stress (ICMR 01029 and ICMR 01031), one pollinator with a negative GCA, and both mapping population parents. The line source resulted in a perfectly linear soil moisture gradient, which was paralleled crop performance in this trial. The results confirmed the previous findings of yield advantage of ICMR 01029 and ICMR 01031 compared to parents H-77/833-2 and PRLT-2/89-33. Leaf gas exchange was measured with LCA04, in three different moisture regimes (row 2, 10 and 18, which were equivalent to control, intermediate and severe stress environments). The photosynthetic rate was significantly correlated with grain yield (r2=0.80), indicating the existence of genotypic differences in the response of leaf gas exchange to drought, which could open new opportunities for better understanding of the plant water relations and selection of drought tolerant varieties in pearl millet.


Bidinger FR., Serraj R, Rizvi SMH, Howarth C, Yadav RS, Hash CT (2004) Field evaluation of drought tolerance QTL effects on phenotype and adaptation in pearl millet [Pennisetum glaucum (L.) R. Br.] topcross hybrids. Field Crops Research submitted.

Bidinger FR, Hash CT (2003) Pearl Millet. In ‘Physiology and Biotechnology Integration in Plant Breeding’ (Eds HT Nguyen, A Blum). pp 225 – 270. (Marcel Dekker: New York)

Bidinger FR, Chandra S, Mahalakshmi V (2000) Genetic improvement of tolerance to terminal drought stress in Pearl Millet [Pennisetum glaucum (L.) R. Br.)]. In ‘Molecular Approaches for the Genetic Improvement of Cereals for Stable Production in Water-Limited Environments’. A Strategic Planning Workshop held at CIMMYT, El Batan, Mexico 21 - 25 June 1999. (Eds JM Ribaut, D Poland) pp 59 – 63. (International Maize and Wheat Improvement Center: Mexico)

Bidinger FR, Mahalakshmi V, Durga Prasada Rao, G (1987) Assessment of drought resistance in pearl millet [Pennisetum americanum (L.) Leeke]. II. Estimation of genotype response to stress. Australian Journal of Agricultural Research 38, 49-59.

Mahalakshmi V, Bidinger FR, Raju DS (1987) Effects of timing of stress in pearl millet. [Pennisetum americanum (L.) Leeke]. Field Crops Research 15, 327-339.

Yadav RS, Hash CT, Bidinger FR, Cavan GP, Howarth CJ (2002) Quantitative trait loci associated with traits determining grain and stover yield in pearl millet under terminal drought stress conditions. Theoretical and Applied Genetics 104, 67-83

Yadav RS, Hash CT, Bidinger FR, Devos KM, Howarth CJ (2004) Genomic regions associated with grain yield and aspects of post-flowering drought tolerance in pearl millet across stress environments and testers background. Euphytica in press

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