Physiologia Plantarum 157: 175–192. 2016 © 2015 Scandinavian Plant Physiology Society, ISSN 0031-9317 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 Hiroyuki Shimono a,* , Akira Abe b , Naohiro Aoki c , Takemasa Koumoto a , Masahiro Sato a , Shuji Yokoi a , Eiki Kuroda a , Takashi Endo d , Ken-ich Saeki d and Kuniaki Nagano d a Crop Science Laboratory, Faculty of Agriculture, Iwate University, 3-18-8, Ueda, Morioka, Iwate 020-8850, Japan b Iwate Biotechnology Research Center, 22-174-4, Narita, Kitakami, Iwate 024-0003, Japan c Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 989-6227,Japan d Miyagi Prefectural Furukawa Agricultural Experiment Station, 88 Fukoku, Oosaki, Furukawa, Miyagi 989-6227, Japan Correspondence *Corresponding author, e-mail: shimn@iwate-u.ac.jp Received 30 July 2015; revised 6 October 2015 doi:10.1111/ppl.12410 Male sterility induced by low temperatures (LTs) during the reproductive stage is a major constraint for temperate zone rice. To detect physiological quanti- tative 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 differen- tially 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 (con- served 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. Abbreviations – AH, Akihikari; AL, anther length; CT, control temperature; DOY, day of year; FRT, spikelet fertility; LT, low temperature; qCTR, QTL for Cold Tolerance at Reproductive stage; qRT-PCR, quantitative real-time polymerase chain reaction; QTL, quantitative trait locus; RIL, recombinant inbred line; ROS, reactive oxygen species; SNP, single nucleotide polymorphism; SSR, simple sequence repeat. Physiol. Plant. 157, 2016 175