Fine mapping of QTL qCTB10-2 that confers cold tolerance at the booting stage in rice

Abstract

The QTL qCTB10 - 2 controlling cold tolerance at the booting stage in rice was delimited to a 132.5 kb region containing 17 candidate genes and 4 genes were cold-inducible. Low temperature at the booting stage is a major abiotic stress-limiting rice production. Although some QTL for cold tolerance in rice have been reported, fine mapping of those QTL effective at the booting stage is few. Here, the near-isogenic line ZL31-2, selected from a BCF population derived from a cross between cold-tolerant variety Kunmingxiaobaigu (KMXBG) and the cold-sensitive variety Towada, was used to map a QTL on chromosome 10 for cold tolerance at the booting stage. Using BCF and BCF populations, we firstly confirmed qCTB10-2 and gained confidence that it could be fine mapped. QTL qCTB10-2 explained 13.9 and 15.9% of the phenotypic variances in those two generations, respectively. Using homozygous recombinants screened from larger BCF and BCF populations, qCTB10-2 was delimited to a 132.5 kb region between markers RM25121 and MM0568. 17 putative predicted genes were located in the region and only 5 were predicted to encode expressed proteins. Expression patterns of these five genes demonstrated that, except for constant expression of LOC_Os10g11820, LOC_Os10g11730, LOC_Os10g11770, and LOC_Os10g11810 were highly induced by cold stress in ZL31-2 compared to Towada, while LOC_Os10g11750 showed little difference. Our results provide a basis for identifying the genes underlying qCTB10-2 and indicate that markers linked to the qCTB10-2 locus can be used to improve the cold tolerance of rice at the booting stage by marker-assisted selection.

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

“…Co-localized and pleiotropic M-QTLs located in adjacent regions on the chromosome govern multiple traits, which are most prominent for the concurrent improvement of multiple traits (Shakiba et al 2017;Li et al 2018;Liang et al 2018). In this study, eight clusters of M-QTLs or pleiotropic M-QTLs were identified on different chromosomes governing simultaneously different traits: .…”

“…These co-localized QTLs were identified in earlier studies on cold tolerance germination and yield component traits in rice (Andaya and Mackill 2003a, b;Koseki et al 2010;Wang et al 2016a;Shakiba et al 2017). Several major lowtemperature germination and seedling-stage QTLs have been distributed widely on all 12 chromosomes using bi-parental mapping populations and diverse rice genetic resources (Teng et al 2001;Chen et al 2006;Liang et al 2006Liang et al , 2018Fujino et al 2008;Pan et al 2015;Jiang et al 2017;Shakiba et al 2017;Li et al 2018). Among the total of 82 M-QTLs, 67% of the M-QTLs received favorable alleles from donor parent HNG, which is significant in LTS tolerance.…”

“…However, despite further progress in the molecular genetic dissection of LTS tolerance in rice, few of them were confirmed to be stable QTLs across environments (Fujino et al 2008;Ji et al 2010;Li et al 2013;Cui et al 2013;Kim et al 2014;Zhu et al 2015). With the development of advanced genomics and molecular marker technology, six QTLs (qCTS-9, qCT8, qCTB7, qCTB3, qCT-3-2, and qCTB10-2) have been finemapped via a map-based cloning approach and only two QTLs (Ctb1 and CTB4a) have been cloned and functionally conferred to LTS (Kuroki et al 2007;Saito et al 2010;Zhou et al 2010;Shirasawa et al 2012;Zhu et al 2015;Li et al 2018;Sun et al 2018). However, even with the different genetic backgrounds of rice germplasm, QTLs for stage-specific cold tolerance were mapped on different locations on the 12 chromosomes.…”

QTL and QTL networks for cold tolerance at the reproductive stage detected using selective introgression in rice

“…Of these, 108 QTLs for CT were detected at the booting stage ( S1 Table ). Four QTLs, qCT8 , qCTB7 , qCTB3 and qCT-3-2 , have been fine mapped [ 6 , 11 – 13 ], qCTB10-2 was delimited to a 132.5 kb region containing 17 candidate genes and 4 genes were cold-inducible [ 14 ], and only two CT QTL, Ctb1 and CTB4a , have been cloned and functionally characterized [ 15 , 16 ]. Ctb1 encodes an F-box protein and functions as part of the E3 ubiquitin ligase complex that is associated with increased spikelet fertility (SF) under cold stress [ 11 ].…”

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

“…For example, rice seedlings exposed to low temperatures exhibit slow development, reduced tillers, yellowish leaves, and rot (Andaya and Mackill 2003). Furthermore, at the reproductive stage, intolerable cold negatively affects panicle growth, fertility and thus results in yield reduction (Li et al 2018). In sum, due to cold stress, rice cannot be grown on approximately 7,000,000 hectares of land in South and Southeast Asia (Sthapit and Witcombe 1998).…”