Mapping quantitative trait loci controlling low-temperature germinability in rice

Abstract

: Low-temperature germination is one of the major determinants for stable stand establishment in the rice direct seeding method in temperate regions and at high altitude areas. Quantitative trait loci (QTL) controlling low-temperature germinability in rice were identified using 96 introgression lines (ILs) derived from a cross between Oryza rufipogon and the Korean japonica cultivar, 'Hwaseongbyeo'. The germination rate at 15℃ was measured to represent low-temperature germination and used for QTL analysis. The germination rate at 15℃ for 7 days of Oryza rufipogon and Hwaseongbyeo was 93.3 and 28.7%, respectively, and that of progenies ranged from 0 to 48%. A linkage map was constructed using 135 simple sequence repeat (SSR) markers. Five putative QTLs associated with low-temperature germination were detected on chromosomes 1, 3, 4, 10 and 11. The QTL, qltg10 on chromosome 10 accounted for 19.2% of the total phenotypic variation for low-temperature germinability. Four additional QTL, accounted for 10.4 -15.1% of the total phenotypic variation. The O. rufipogon alleles in all detected QTLs loci increased the low-temperature germination rate. No QTL associated with low temperature germinability has been detected near the qltg10 QTL in this study suggesting that qltg10 is a new QTL. The locus, qltg10 is of particular interest because of its independence from undesirable height and maturity effects. The DNA markers linked to the QTL for low temperature germinability would be useful in selecting lines with enhanced low temperature germinability in rice breeding program.

Characterization of a New qLTG3–1 Allele for Low-temperature Germinability in Rice from the Wild Species Oryza rufipogon

“…Germination tests were conducted as described by Nguyen et al (2012) with minor modifications. Seeds of the F 2 plants were collected 45 days after flowering.…”

“…LTG is controlled by QTLs which have been detected using biparental populations and association analysis (Miura et al 2001;Fujino et al 2004;Jiang et al 2006;Fujino et al 2008;Ji et al 2009;Nguyen et al 2012;Fujino et al 2015;Hyun et al 2015;Wang et al 2018). LTG QTLs have been identified on all 12 rice chromosomes, but many have relatively small effects, explaining less than 20% of the phenotypic variance.…”

“…QTL-QTL or gene-gene interactions need to be examined (Mackay 2014). Previous QTL studies mainly focused on identifying single locus genes, while studies on the interactions between genotypes at two or more QTL for LTG are limited (Miura et al 2001;Fujino et al 2004;Jiang et al 2006;Fujino et al 2008;Ji et al 2009;Nguyen et al 2012;Fujino et al 2015).…”

“…Previously, we mapped two QTLs, qLTG1 and qLTG3, that controlled low-temperature germinability, using a BC 4 F 8 population derived from an interspecific cross between a Korean elite cultivar Hwaseong and O. rufipogon (IRGC 105491) (Nguyen et al 2012;Shim et al 2019).…”

Characterization of Quantitative Trait Loci for Germination and Coleoptile Length under Low-Temperature Condition Using Introgression Lines Derived from an Interspecific Cross in Rice

“…In our previous study, five QTLs for low-temperature germinability, qLTG1 , qLTG3 , qLTG4 , qLTG10 , and qLTG11 were mapped using a BC 4 F 8 population including 96 introgression lines (ILs) derived from an interspecific cross between a Korean elite line Hwaseong and O. rufipogon [ 27 ]. Recently, qLTG1 was fine mapped using introgression lines and the new qLTG3-1 allele of the O. rufipogon was identified [ 28 , 29 ].…”