Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits.

Prashant Vikram,B P Mallikarjuna Swamy,Arvind Kumar,N K Singh,Amelia Henry,Ajay Kohli,Bikram P Singh,Shalabh Dixit,Berta Miro,Renu Singh

doi:10.1038/srep14799

Prashant Vikram, B P Mallikarjuna Swamy + Show 8 more

Open Access

https://doi.org/10.1038/srep14799

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Abstract

Green Revolution (GR) rice varieties are high yielding but typically drought sensitive. This is partly due to the tight linkage between the loci governing plant height and drought tolerance. This linkage is illustrated here through characterization of qDTY1.1, a QTL for grain yield under drought that co-segregates with the GR gene sd1 for semi-dwarf plant height. We report that the loss of the qDTY1.1 allele during the GR was due to its tight linkage in repulsion with the sd1 allele. Other drought-yield QTLs (qDTY) also showed tight linkage with traits rejected in GR varieties. Genetic diversity analysis for 11 different qDTY regions grouped GR varieties separately from traditional drought-tolerant varieties, and showed lower frequency of drought tolerance alleles. The increased understanding and breaking of the linkage between drought tolerance and undesirable traits has led to the development of high-yielding drought-tolerant dwarf lines with positive qDTY alleles and provides new hope for extending the benefits of the GR to drought-prone rice-growing regions.

Highlights

Rice demand in the coming decades[7]
To determine whether the drought tolerance conferred by qDTY1.1 was due to a pleiotropic effect of the sd[1] gene or whether there was a tight genetic linkage between qDTY1.1 and sd[1] genes, a two-way approach was undertaken: (i) statistical analysis of multiple traits for linkage vs pleiotropy by saturation mapping in the recombinant inbred line (RIL) mapping populations used for the identification of qDTY1.1, and (ii) fine mapping of the qDTY1.1 locus using region-specific single nucleotide polymorphism (SNP) markers in a large backcross inbred line (BIL) population
A re-mapping of the qDTY1.1 QTL interval (RM11943–RM431) in the three N22-derived RIL populations (N22/Swarna, N22/IR64, and N22/MTU1010) using three additional SNP markers in the region revealed that qDTY1.1 was located distal to the sd[1] gene (Fig. 1, Table 2)

Summary

Introduction

Rice demand in the coming decades[7]. Genetic improvement of rice for increased adaptation to rainfed environments can significantly help to fill this gap and improve food security in Asia and Africa. One of the reasons for this could be the linkage/pleiotropic action of abiotic stress tolerance genes to traits that were considered undesirable, such as low yield potential, tall height, poor grain quality, etc., leading to their elimination from GR varieties during the selection process. The qDTY1.1 effect on grain yield under drought was predicted to be either because of the pleiotropic effects of the sd[1] gene itself or due to a separate locus within the qDTY1.1 region tightly linked to sd[115–18] Both cases are a concern for breeding efforts to improve the drought tolerance of GR varieties, since linkage of qDTY1.1 and sd[1] would indicate that the drought tolerance allele could have been lost in developing dwarf varieties, and pleiotropy would indicate that drought susceptibility and dwarfness cannot be separated. We aimed to break the linkage between qDTY1.1 and the tall allele of sd[1], as well as between other qDTY and undesirable traits, to develop high-yielding drought-tolerant rice varieties

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