Locating QTLs controlling overwintering seedling rate in perennial glutinous rice 89-1 (Oryza sativa L.)

Abstract

A new cold tolerant germplasm resource named glutinous rice 89-1 (Gr89-1, Oryza sativa L.) can overwinter using axillary buds, with these buds being ratooned the following year. The overwintering seedling rate (OSR) is an important factor for evaluating cold tolerance. Many quantitative trait loci (QTLs) controlling cold tolerance at different growth stages in rice have been identified, with some of these QTLs being successfully cloned. However, no QTLs conferring to the OSR trait have been located in the perennial O. sativa L. To identify QTLs associated with OSR and to evaluate cold tolerance. 286 F recombinant inbred lines (RILs) derived from a cross between the cold tolerant variety Gr89-1 and cold sensitive variety Shuhui527 (SH527) were used. A total of 198 polymorphic simple sequence repeat (SSR) markers that were distributed uniformly on 12 chromosomes were used to construct the linkage map. The gene ontology (GO) annotation of the major QTL was performed through the rice genome annotation project system. Three main-effect QTLs (qOSR2, qOSR3, and qOSR8) were detected and mapped on chromosomes 2, 3, and 8, respectively. These QTLs were located in the interval of RM14208 (35,160,202 base pairs (bp))-RM208 (35,520,147 bp), RM218 (8,375,236 bp)-RM232 (9,755,778 bp), and RM5891 (24,626,930 bp)-RM23608 (25,355,519 bp), and explained 19.6%, 9.3%, and 11.8% of the phenotypic variations, respectively. The qOSR2 QTL displayed the largest effect, with a logarithm of odds score (LOD) of 5.5. A total of 47 candidate genes on the qOSR2 locus were associated with 219 GO terms. Among these candidate genes, 11 were related to cell membrane, 7 were associated with cold stress, and 3 were involved in response to stress and biotic stimulus. OsPIP1;3 was the only one candidate gene related to stress, biotic stimulus, cold stress, and encoding a cell membrane protein. After QTL mapping, a total of three main-effect QTLs-qOSR2, qOSR3, and qOSR8-were detected on chromosomes 2, 3, and 8, respectively. Among these, qOSR2 explained the highest phenotypic variance. All the QTLs elite traits come from the cold resistance parent Gr89-1. OsPIP1;3 might be a candidate gene of qOSR2.

Global Analysis of Gene Expression Profiles in Glutinous Rice 89-1 (Oryza sativa L.) Seedlings Exposed to Chilling Stress

“…Glutinous rice 89-1 (Gr89-1) has overwintering ability and germinates through axillary buds during the following spring. Yields are the same as in a normal season (up to 6.29 t/hm 2 ) in Chongqing, China (Deng et al 2018). Other studies have revealed similar overwintering ability of Oryza longistaminata and Dongxiang wild rice (O. rufipogon) in south and southwest China (He et al 1996;Liang et al 2017;Mao et al 2015;Zhang et al 2017a, b).…”

Study on tillering stage cold tolerant response in overwintering cultivated rice via comparative transcriptomic

“…In previous studies, QTLs for overwinter germination rate (qPOG‐2, qPOG‐3, and qPOG‐7; Zhao et al, 2012) and overwinter emergence rate (qOSR2, qOSR3, and qOSR8; Deng et al, 2018) were localized in Gr 89‐1. In this study, all genes within the QTL loci were matched with NCBI and RAP‐DB databases to obtain 398 annotated genes.…”

“…Cultivar rice "Glutinous rice 89-1" (Gr 89-1) is an exceptional overwintering cold-tolerant germplasm resource originating from Chongqing, China (Zhao et al, 2007), whose axillary buds can withstand low temperatures at different altitudes and germinate the following year. Genetic studies have been conducted on the cold tolerance traits of Gr 89-1, including QTL localization of ratooning germinability (PRG), overwintering germinability (POG; Zhao et al, 2012), overwintering seedling rate (OSR; Deng et al, 2018), and global analysis of 3-leaf stage seedlings of Gr 89-1 exposed to a cold treatment (Pan et al, 2016). Here, RNA-seq was performed using another common indica cultivar rice, "R07," as cold intolerant comparator to explore the phenotype, physiology, transcriptome network, and cold tolerance mechanism of Gr 89-1.…”

Regulatory effect of exogenous melatonin on the expression of enzyme genes in the AsA-GSH cycle and nitrogen metabolism in rice seedlings under NaCl stress

“…Glutinous rice 89-1 is an overwintering rice variety, as its axillary buds are dormant during the winter and can germinate and regenerate the following spring. The yield of overwintering regeneration season is equivalent to that of current season (Deng et al, 2018;Chen et al, 2021). After cleaning and disinfection, 100 rice seeds were selected and placed in the germination box (10 rows × 10 columns), which was transferred to a light incubator under the conditions of 16 h light/8 h dark, 30 °C, and 70% humidity for 10 d. Seedlings were cultivated for three-and one-heart periods, and seedlings with consistent growth were used for the next treatment.…”