Combining mapping of physiological quantitative trait loci and transcriptome for cold tolerance for counteracting male sterility induced by low temperatures during reproductive stage in rice

Abstract

Male sterility induced by low temperatures (LTs) during the reproductive stage is a major constraint for temperate zone rice. To detect physiological quantitative trait loci (QTLs), we modeled genotypic variation in the physiological processes involved in low temperature spikelet sterility on the basis of anther length (AL), a proxy for microspore and pollen grain number per anther. The model accounted for 83% of the genotypic variation in potential AL at normal temperature and the ability to maintain AL at LT. We tested the model on 208 recombinant inbred lines of cold-tolerant 'Tohoku-PL3' (PL3) × cold-sensitive 'Akihikari' (AH) for 2 years. QTLs for spikelet fertility (FRT) at LT were detected on chromosomes 5 (QTL for Cold Tolerance at Reproductive stage, qCTR5) and 12 (qCTR12). qCTR12 was annotated with the ability to maintain AL under LTs. qCTR5 was in a region shared with QTLs for culm length and heading date. Genome-wide expression analysis showed 798 genes differentially expressed in the spikelets between the parents at LTs. Of these, 12 were near qCTR5 and 23 were near qCTR12. Gene expression analysis confirmed two candidate genes for qCTR5 (O-methyltransferase ZRP4, Os05g0515600; beta-1,3-glucanase-like protein, Os05g0535100) and one for qCTR12 (conserved hypothetical protein, Os12g0550600). Nucleotide polymorphisms (21 deletions, 2 insertions and 10 single nucleotide polymorphisms) in PL3 were found near the candidate conserved hypothetical protein (Os12g0550600) and upstream in PL3, but not in AH. Haplotype analysis revealed that this gene came from 'Kuchum'. The combination of mapping physiological QTLs with gene expression analysis can be extended to identify other genes for abiotic stress response in cereals.

Regulatory Networks in Pollen Development under Cold Stress

“…Plants exposed to CS show abnormal pollen development in anthers, “often producing distorted anthers or sterile pollen grains” thereby resulting in “reduced fertilization” ( Nayyar et al, 2005 ; Oda et al, 2010 ; Thakur et al, 2010 ; Shimono et al, 2016 ). The most sensitive stages to CS are, “after the onset of meiosis and pollen maturation” ( Boyer and McLaughlin, 2007 ).…”

A quartet pollen phenotype identified in a population of Brassica interspecific hybrids shows incomplete penetrance and variable response to temperature

“…; Shimono et al . ), particularly in the period after initiation of meiotic division and during pollen maturation (Boyer & McLaughlin ). Cold temperatures may also cause an increase in formation of 2n diploid gametes (Ramsey & Schemske ; Otto & Whitton ; Mason et al .…”

“…Decreases in temperature typically reduce the growth rate, leading to delayed flowering and concomitantly delayed seed development at later growth stages under suboptimal temperature conditions (Zinn et al 2010). Low temperature stress can also cause damage to male reproductive organs (where anthers may be partially distorted) leading to the failure of normal pollen formation and decreased fertilisation (Oda et al 2010;Thakur et al 2010;Shimono et al 2016), particularly in the period after initiation of meiotic division and during pollen maturation (Boyer & McLaughlin 2007). Cold temperatures may also cause an increase in formation of 2n diploid gametes (Ramsey & Schemske 1998;Otto & Whitton 2000;Mason et al 2011).…”

Transcriptome Analysis for Abiotic Stresses in Rice (Oryza sativa L.)

“…The high salt concentration disrupts the ability of roots for efficient water uptake, leading to perturbation of crucial metabolic reactions inside the cell restricting plant growth and yield potential [8]. Low temperature reduces germination, causes poor establishment, delays phenological development, and increases spikelet sterility [9], and other physiological and metabolite changes causing low yield [10]. Furthermore, rice can tolerate partial submergence as paddy rice or deepwater rice because it is very well adapted to waterlogged conditions as it has well-developed aerenchyma that facilitates oxygen diffusion and prevents anoxia in roots [11][12][13].…”