Saturation mapping of QTL regions and identification of putative candidate genes for drought tolerance in rice

Abstract

We have developed 85 new markers (50 RFLPs, 5 SSRs, 12 DD cDNAs, 9 ESTs, 8 HSP-encoding cDNAs and one BSA-derived AFLP marker) for saturation mapping of QTL regions for drought tolerance in rice, in our efforts to identify putative candidate genes. Thirteen of the markers were localized in the close vicinity of the targeted QTL regions. Fifteen of the additional markers mapped, respectively, inside one QTL region controlling osmotic adjustment on chromosome 3 ( oa3.1) and 14 regions that affect root traits on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 10 and 12. Differential display was used to identify more putative candidate genes and to saturate the QTL regions of the genetic map. Eleven of the isolated cDNA clones were found to be derived from drought-inducible genes. Two of them were unique and did not match any genes in the GenBank, while nine were highly similar to cDNAs encoding known proteins, including a DnaJ-related protein, a zinc-finger protein, a protease inhibitor, a glutathione-S-transferase, a DNA recombinase, and a protease. Twelve new cDNA fragments were mapped onto the genetic linkage map; seven of these mapped inside, or in close proximity to, the targeted QTL regions determining root thickness and osmotic adjustment capacity. The gene I12A1, which codes for a UDP-glucose 4-epimerase homolog, was identified as a putative target gene within the prt7.1/brt7.1 QTL region, as it is involved in the cell wall biogenesis pathway and hence may be implicated in modulating the ability of rice roots to penetrate further into the substratum when exposed to drought conditions. RNAs encoding elongation factor 1beta, a DnaJ-related protein, and a homolog of wheat zinc-finger protein were more prominently induced in the leaves of IR62266 (the lowland rice parent of the mapping materials used) than in those of CT9993 (the upland rice parent) under drought conditions. Homologs of 18S ribosomal RNA, and mRNAs for a multiple-stress induced zinc-finger protein, a protease inhibitor, and a glutathione-S-transferase were expressed at significantly higher levels in CT9993 than in IR62266. Thus several genes involved in the regulation of DNA structure and mRNA translation were found to be drought-regulated, and may be implicated in drought resistance.

Drought-tolerance QTLs commonly detected in two sets of reciprocal introgression lines in rice

“…The QTL QSnp3a governing SpNP was localised in the region of 3502670-4681740 on chromosome 3 and was mapped together with the rn3 for root number in PVC-pipe at mature stage (Qu et al 2008), QRvd3 for root volume, and QRgvd3 for root growth rate in volume under drought conditions (Yue et al 2006), as well as the QTL for leaf rolling score in paddy soil condition (Yue et al 2005). The QTL QSf8 influencing SF detected in the region of 19556500-20662759 on chromosome 8 was mapped together with QTLs for several DT related traits in rice across a variety of genetic backgrounds and environments, such as oa8.1 for osmotic adjustment (Nguyen et al 2004), the QTL for relative water content (Price et al 2002a), the QTL for leaf drying (Babu et al 2003), the QTL for drought response index (DRI) (Yue et al 2005), and QGy8 for grain yield under stress. The QTL QSnp11 affecting SpNP, which was located in the region of 749467-1767997 on chromosome 11, was mapped together with the QMrdd11 affecting maximum root depth and QDrvd11 for deep root rate in volume under drought conditions (Yue et al 2006) and QTLs for panicle number, filled grains per panicle, seed fertility and grain yield per plant simultaneously detected under drought and irrigated conditions at reproductive stage (Wang et al 2013).…”

Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database

“…At least 24 papers have been published in the last 10 years on quantitative trait locus (QTL) detection for a large number of root parameters in several populations and different growth conditions (Champoux et al 1995;Ray et al 1996;Redona and Mackill 1996;Yadav et al 1997;Price et al 1999Price et al , 2000Price et al , 2002Ali et al 2000;Hemamalini et al 2000;Tripathy et al 2000;Zheng et al 2000Zheng et al , 2003Shen et al 2001;Zhang et al 2001a, b;Kamoshita et al 2002a, b;Courtois et al 2003;Nguyen et al 2004;Xu et al 2004;Li et al 2005b;Horii et al 2006;Yue et al 2006;MacMillan et al 2006).…”

Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome

“…The genes; galE(3) (COLAER_01955), murB(3) (COLAER_01957) and mazG(3) (COLAER_01981), encode hypothetical proteins similar to UDP-glucose 4-epimerase (GalE), UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) and nucleoside triphosphate pyrophosphohydrolase (MazG family protein). Although GalE has been tentatively linked to salt tolerance in previous studies (Hengge-Aronis et al, 1991;Bohringer et al, 1995;Nguyen et al, 2004) we are unaware of any previous link between MurB or MazG and bacterial salt tolerance.…”

“…Indeed, sequences representing at least eight uncharacterized species of the genus Akkermansia have been identified from different gut metagenomic libraries (van Passel et al, 2011). Interestingly, a UDP glucose 4-epimerase homologue has been identified as a putative gene involved in drought tolerance in rice by modulating the ability of rice roots to penetrate deeper into the substratum when exposed to drought conditions (Nguyen et al, 2004).…”