Abstract
BackgroundIn the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. However, identification of most precise and consistent QTL across the environments and genetics backgrounds is essential for their successful use in Marker-assisted Selection. In this study, an attempt was made to locate consistent QTL regions associated with yield increase under drought by applying a genome-wide QTL meta-analysis approach.ResultsThe integration of 15 maps resulted in a consensus map with 531 markers and a total map length of 1821 cM. Fifty-three yield QTL reported in 15 studies were projected on a consensus map and meta-analysis was performed. Fourteen meta-QTL were obtained on seven chromosomes. MQTL1.2, MQTL1.3, MQTL1.4, and MQTL12.1 were around 700 kb and corresponded to a reasonably small genetic distance of 1.8 to 5 cM and they are suitable for use in marker-assisted selection (MAS). The meta-QTL for grain yield under drought coincided with at least one of the meta-QTL identified for root and leaf morphology traits under drought in earlier reports. Validation of major-effect QTL on a panel of random drought-tolerant lines revealed the presence of at least one major QTL in each line. DTY12.1 was present in 85% of the lines, followed by DTY4.1 in 79% and DTY1.1 in 64% of the lines. Comparative genomics of meta-QTL with other cereals revealed that the homologous regions of MQTL1.4 and MQTL3.2 had QTL for grain yield under drought in maize, wheat, and barley respectively. The genes in the meta-QTL regions were analyzed by a comparative genomics approach and candidate genes were deduced for grain yield under drought. Three groups of genes such as stress-inducible genes, growth and development-related genes, and sugar transport-related genes were found in clusters in most of the meta-QTL.ConclusionsMeta-QTL with small genetic and physical intervals could be useful in Marker-assisted selection individually and in combinations. Validation and comparative genomics of the major-effect QTL confirmed their consistency within and across the species. The shortlisted candidate genes can be cloned to unravel the molecular mechanism regulating grain yield under drought.
Highlights
In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice
Overview of QTL and development of a consensus map In the 15 populations of rice screened for drought tolerance to map QTL, population size ranged from 150 [22] to 436 lines [5]
The phenotypic variance of the initial QTL varied from 3.2% to 40% and the confidence interval of the markers varied from 2 to 30 cM
Summary
In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. Most of the QTL for grain yield under drought have been mapped against a single genetic background in early-segregating generations (F3, BC2, and BC2F2) evaluated in a limited number of environments. Such QTL may not provide a consistent effect because of variation in the genetic background and environment. The QTL may not be transferrable to other backgrounds because of unfavorable epistatic interactions resulting in reduced or even no effects in a new genetic background [6,7] Considering all these facts, it is difficult to predict the usefulness of QTL for MAS based only on their performance in an individual genetic background in any particular study
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