Natural variation in the HAN1 gene confers chilling tolerance in rice and allowed adaptation to a temperate climate

Abstract

Rice (Oryza sativa L.) is a chilling-sensitive staple crop that originated in subtropical regions of Asia. Introduction of the chilling tolerance trait enables the expansion of rice cultivation to temperate regions. Here we report the cloning and characterization of HAN1, a quantitative trait locus (QTL) that confers chilling tolerance on temperate japonica rice. HAN1 encodes an oxidase that catalyzes the conversion of biologically active jasmonoyl-L-isoleucine (JA-Ile) to the inactive form 12-hydroxy-JA-Ile (12OH-JA-Ile) and fine-tunes the JA-mediated chilling response. Natural variants in HAN1 diverged between indica and japonica rice during domestication. A specific allele from temperate japonica rice, which gained a putative MYB cis-element in the promoter of HAN1 during the divergence of the two japonica ecotypes, enhances the chilling tolerance of temperate japonica rice and allows it to adapt to a temperate climate. The results of this study extend our understanding of the northward expansion of rice cultivation and provide a target gene for the improvement of chilling tolerance in rice.

Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa

“…Several other genes are also of value for improving rice resistance to abiotic stresses. These included three cloned genes (COLD1, bZIP73, and HAN1) for cold tolerance at seedling stage (Ma et al 2015;Liu et al 2018b;Mao et al 2019), CTB4a for cold tolerance at the booting stage (Zhang et al 2017a) and TT1 for high-temperature resistance (Li et al 2015). Although many genes for stress resistance have been cloned, the most successful application of these cloned stress tolerance genes in rice breeding was SUB1 for submergence tolerance.…”

Coordination of light, circadian clock with temperature: The potential mechanisms regulating chilling tolerance in rice

“…Usually, determination of chilling tolerance in rice at seedling stage uses the survival rates of rice seedlings after chilling treatment as the primary indicator (Ma et al 2015; Lv et al 2017; Zhang et al 2017b; Liu et al 2018a; Mao et al 2019). Identification of chilling tolerance at booting stage is typically determined based on yield traits such as seed setting rates and relative seed setting rates, together with pollen fertility (Zhang et al 2017b; Liu et al 2019).…”

“…Overexpression of CTB4a correlates with increased ATP synthase activity through CTB4a‐AtpB (a beta subunit of ATP synthase) interaction and concomitantly higher ATP levels, enhanced pollen fertility and seed setting rate, and improved yield under chilling stress conditions (Zhang et al 2017b) (Figure ). COLD1 and HAN1 were identified using a large mapping population derived from a cross between chilling‐tolerant variety Nipponbare and chilling‐sensitive variety 93‐11, chilling‐tolerant variety 02428, and chilling‐sensitive variety Teqing, respectively (Ma et al 2015; Mao et al 2019). Importantly, natural variations of COLD1 , CTB4a , and HAN1 occurred to enhance rice adaption to cold habitats (Ma et al 2015; Zhang et al 2017b; Mao et al 2019).…”

“…COLD1 and HAN1 were identified using a large mapping population derived from a cross between chilling‐tolerant variety Nipponbare and chilling‐sensitive variety 93‐11, chilling‐tolerant variety 02428, and chilling‐sensitive variety Teqing, respectively (Ma et al 2015; Mao et al 2019). Importantly, natural variations of COLD1 , CTB4a , and HAN1 occurred to enhance rice adaption to cold habitats (Ma et al 2015; Zhang et al 2017b; Mao et al 2019). OsbZIP73 , another gene facilitating adaptation of japonica rice to cold climates, was identified through association studies, population genetics and stress‐response profiling (Liu et al 2018a).…”

Studies on plant responses to environmental change in China: the past and the future

“…此外, 通过对藜麦基因 组的组装和盐泡细胞的转录组分析, 揭示了藜麦耐盐 和高营养价值的分子机制 [89] . [94] 和CTB4a(cold tolerance at booting stage) [95] ; 通…”