Low-temperature Germinability In Rice Research Articles

Tamyb10-D1 restores red grain color and increases grain dormancy via suppressing expression of TaLTP2.128, non-specific lipid transfer protein in wheat

Grain dormancy of wheat is closely associated with grain color: red-grained lines show higher dormancy than white-grained lines. The production of red pigments is regulated by R-1, Tamyb10 gene. However, the relation between grain color and dormancy remains unknown. For this study, we generated transgenic lines which were introduced a DNA fragment containing Tamyb10-D1 gene and its a 2 kb promoter including the 5′ untranslated region into white-grained wheat. Transgenic lines showed red-grained and higher dormant traits. Contents of plant hormones and gene expression of embryos at 30 days after pollination were examined in a wild type and a transgenic line. No differences were observed in the contents of plant hormones, but several genes are differentially expressed between these lines. One differentially expressed gene, TaLTP2.128, is a member of non-specific lipid transfer proteins. It was expressed higher in white grains than in red grains. A putative amino acid sequence showed similarity to that of OsHyPRP5, which is identified as QTL controlling low-temperature germinability in rice. Expression of TaLTP2.128 was increased by grain imbibition. The increasing levels were higher not only in other white-grained lines, but also in non-dormant red-grained lines. TaLTP2.128 was expressed at a quite early stage of germination. These study findings indicate that Tamyb10 regulates dormancy release by the modification of TaLTP2.128 acting as trigger of germination.

Brassinosteroid biosynthesis gene OsD2 is associated with low-temperature germinability in rice.

In rice, low-temperature germinability (LTG) is essential for stable stand establishment using the direct seeding method in temperate and high-altitude areas. Previously, we reported that the quantitative trait locus qLTG1 is associated with LTG. qLTG1 is also associated with tolerance to several abiotic stresses, such as salt and osmotic conditions. In this study, map-based cloning and sequence analysis indicated that qLTG1 is allelic to DWARF2 (OsD2), which encodes cytochrome P450 D2 (LOC_Os01g10040) involved in brassinosteroid (BR) biosynthesis. Sequence comparison of the two parental lines, Hwaseong and Oryza rufipogon (IRGC 105491), revealed five single nucleotide polymorphisms (SNPs) in the coding region. Three of these SNPs led to missense mutations in OsD2, whereas the other two SNPs were synonymous. We evaluated two T-DNA insertion mutants, viz., overexpression (OsD2-OE) and knockdown (OsD2-KD) mutants of OsD2, with the Dongjin genetic background. OsD2-KD plants showed a decrease in LTG and grain size. In contrast, OsD2-OE plants showed an increase in grain size and LTG. We also examined the expression levels of several BR signaling and biosynthetic genes using the T-DNA insertion mutants. Gene expression analysis and BR application experiments demonstrated that BR enhanced the seed germination rate under low-temperature conditions. These results suggest that OsD2 is associated with the regulation of LTG and improving grain size. Thus, OsD2 may be a suitable target for rice breeding programs to improve rice yield and LTG.

Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

Low-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment substitution lines (SSSLs) was used to conduct a genetic dissection for LTG across four cropping seasons. LTG was a typical quantitative trait with a high combined broad-sense heritability of 0.71. By comparison with the recipient parent, Huajingxian74, 24 SSSLs were identified as carrying LTG QTLs, which were further merged into integrated QTLs with shorter genetic distances by substitution mapping. Finally, 14 LTG QTLs were mapped on ten chromosomes, including seven positive-effect and seven negative-effect QTLs, with additive effect contributions ranging from 19.2 to 39.9%. qLTG3a, a main-effect and novel QTL, was confirmed by bulk segregant analysis using an F2 segregating population, and five key recombinants were selected to develop F3 populations for progeny testing. Marker-trait association analysis fine mapped qLTG3a to a 332.7-kb physical region between markers M6026 and M6341. Within this interval, 40 annotated genes were revealed, and three genes (Os03g0213300, Os03g0214400, and Os03g0214600) were considered as pivotal candidate genes for qLTG3a based on their sequence variations and expression patterns. Besides low temperature, qLTG3a can also enhance seed germination under standard temperature and osmotic stress. In summary, this study identified some genetic factors regulating LTG and opened a new window for breeding elite direct-seeded rice varieties. It will help reduce the climate risk in the production process of rice, which is of great significance to ensuring food security.

Mapping QTLs controlling low-temperature germinability in rice by using single segment substitution lines derived from 4 AA-genome species of wild rice

Rice growth is sensitive to low temperature. Chilling injury is one of the main natural disasters in rice cultivation, and is damaging to rice growth at all developmental stages. Low-temperature germinability (LTG) is an important trait for seedling establishment, especially in rice direct-sowing practice. However, the genetic mechanism of LTG remains elusive. Here, we report the mapping of QTLs controlling LTG in rice using 586 single segment substitution lines (SSSL) derived from 4 AA-genome wild rice species. 21 SSSLs with the highest germination rate at low temperature in both of the two tested seasons were selected, from them 10 QTLs controlling LTG were identified by substitution mapping to locate on 6 chromosomes: chromosome 1, 3, 5, 7, 8 and 11, with an interval length of 3.45 to 20.15 cM. Five QTLs were detected from Niv-SSSls: qLTGn3-1, qLTGn5-1, qLTGn5-3, qLTGn7-1 and qLTGn7-2, their additive effects ranged from 3.72% to 19.74% in late season 2018. qLTGb1-1 and qLTGb8-2 were detected in the SSSLs with O. barthii as the donor and they accounted for at least 9.51% of the total phenotypic variation. Two QTLs, qLTGg5-2 and qLTGg8-1, were derived from O. glumaepatula, and their average additive effects were 4.28% and 20.39% in late seasons 2018, respectively. qLTGm11-1 on chromosome 11 was the only QTL identified from O. meridionalis. All QTLs derived from wild rice species improved low-temperature germination significantly. The SSSL library with wild rice species as donor is therefore a valuable resource for rice germplasm innovation and the breeding of chilling-resistant varieties.

The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.)

BackgroundDirect seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far.ResultsIn the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2 showed that there were large LTG variations within the population, and the LTG of Indica group was significantly higher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified through genome-wide association study (GWAS). Among them, qLTG_sRDP2–3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2–12 are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2–10a had the largest contribution to LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). The presence of qLTG_sRDP2–10a could result in 59.8% increase in LTG under 15 °C low temperature. The expression analysis of the genes within qLTG_sRDP2–10a region indicated that LOC_Os10g22520 and LOC_Os10g22484 exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed that there were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, and an about 6 kb variation at the 3′ end of LOC_Os10g22484 between the high and low LTG lines, suggesting that the sequence variations of the two genes could be the cause for their differential expression in high and low LTG lines.ConclusionAmong the 11 QTLs identified in this study, qLTG_sRDP2–10a could also be detected in other three studies using different germplasm under different cold environments. Its large effect and stable expression make qLTG_sRDP2–10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, were considered as the candidate genes underlying qLTG_sRDP2–10a. Our results suggest that integrating GWAS and SSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2–10a and its candidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.

Fine Mapping of a Low-Temperature Germinability QTLqLTG1Using Introgression Lines Derived fromOryza rufipogon

Low-temperature germinability (LTG) is an important trait for rice direct seeding at temperate and high-altitude region. Previously, five QTLs (quantitative trait loci) for LTG were detected using an interspecific cross population between the Korea japonica cultivar Hwaseong and Oryza rufipogon (IRGSP#105491). O. rufipogon alleles at all loci increased the germination rate at the 13℃ condition. In this study, we tried to confirm and fine-map qLTG1 located on the short arm of chromosome 1. To map the qLTG1, two introgression lines, TR5 and TR20 were crossed to Hwaseong to develop F2:3 populations. QTL analysis confirmed the existence of the qLTG1 and it explained 55.5% and 29.9% of phenotypic variation in two populations, respectively. Substitution mapping using informative recombinant lines indicated that qLTG1 was located in 167-kb region between two SSR markers RM10310 and RM10326. This segment harbored 18 genes with nine of them were annotated with specific gene function. In addition, the O. rufipogon introgression in this region was associated with an increase in spikelets per panicle in the Hwaseong background. The results strongly indicate that the O. rufipogon alleles will be a valuable source of genes in improving japonica rice for low-temperature germinability and yield. To our knowledge, this is the first report to fine-map qLTG1 associated with LTG in rice considering that no QTL for LTG has not been reported near this QTL region from other biparental populations.

Development of low-temperature germinability markers for evaluation of rice (Oryza sativa L.) germplasm

Low-temperature germinability (LTG) is an important trait for breeding of varieties for use in direct-seeding rice production systems. Although rice (Oryza sativa L.) is generally sensitive to low temperatures, genetic variation for LTG exists and several quantitative trait loci (QTLs) have been reported. Most notably, the gene underlying the major effect QTL qLTG3-1 has been cloned and implicated in tissue weakening. The objective of this study was to develop molecular markers for use in selecting rice germplasm with enhanced LTG. A panel of japonica rice accessions (n = 180) from temperate regions in Asia was evaluated for LTG and genotyped with markers from qLTG3-1 and regions previously reported to harbor other LTG QTLs. In addition to the germplasm evaluation using these markers, an association analysis was conducted using SNP data generated by reduced representation sequencing of the panel. Eight SNP markers were found to be significantly associated with LTG using general and mixed linear models. Two of these markers were in close proximity (~35 kb) to each other on chromosome 4 in a region previously linked to LTG in rice. The identification of several markers strongly associated with LTG in locations not previously reported provides a foundation for further genetic dissection of this complex trait.

Mapping quantitative trait loci controlling low-temperature germinability in rice

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 <TEX>$15^{\circ}C$</TEX> was measured to represent low-temperature germination and used for QTL analysis. The germination rate at <TEX>$15^{\circ}C$</TEX> 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.

Origins of functional nucleotide polymorphisms in a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice

qLTG3-1 is a major quantitative trait locus (QTL) controlling tolerance to low-temperature at the seed germination stage (termed low-temperature germinability) in rice using a population derived from the cross between Italica Livorno from Italy and Hayamasari from Japan. Map-based cloning identified that qLTG3-1 encodes a protein of unknown function. The molecular identification of this major QTL could make it possible to identify allelic variation and favorable alleles for rice breeding programs. The present study examined the identification of qLTG3-1 alleles and their distribution among 62 landraces of Asian cultivated rice (Oryza sativa L.) collected from 19 different countries, termed the rice core collection. In the coding region, a single non-synonymous substitution and 3 in-frame insertion/deletion polymorphisms (indels) were detected. The almost completely conserved protein alignment of qLTG3-1 was also identified among 5 Oryza species, suggesting that the function of qLTG3-1 is critical for seed germination or for rice growth by pleiotropic effects of the gene. The functional nucleotide polymorphisms (FNPs), a 71-bp deletion found in Hayamasari and an amino acid substitution found in Nipponbare, was identified in varieties from Japan. These alleles with FNPs might be adapted to rice cultivation in specific local conditions. The present results may contribute to the utilization of favorable alleles of qLTG3-1 for the improvement of low-temperature germinability in rice breeding programs.

Genetic effects of major QTLs controlling low-temperature germinability in different genetic backgrounds in rice (Oryza sativaL.)

The effects of QTLs are demonstrated basically within the population used in the original QTL analysis as the difference between the alleles of the parental varieties. For the efficient use of QTLs in breeding programs, it is necessary to assess whether the QTL exhibits its genetic effect when it is introgressed into different genetic backgrounds. Extensive studies of tolerance to low temperature at the seed germination stage (called low-temperature germinability) in rice revealed that 2 major QTLs on chromosomes 3 and 11, qLTG3-1 and qLTG11, have large effects. This study assessed the effects of these 2 QTLs from an aus variety, Kasalath, in different genetic backgrounds of 3 japonica varieties, Hoshinoyume, Hayamasari, and Koshihikari. Backcrossed progenies and chromosome segment substitution lines showed that both qLTG3-1 and qLTG11 were effective in the Hoshinoyume and Koshihikari backgrounds, while only qLTG3-1 was effective in the Hayamasari background. The results in this study demonstrated that these 2 QTLs are useful for the improvement of low-temperature germinability in rice breeding programs. The results also indicated that low-temperature germinability in rice is governed by an epistatic interaction of qLTG11.

Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice

The control of seed germination under environmental conditions, where plants will be grown, is important for the adaptability of plants. Low-temperature is one of the most common environmental stress factors that affect plant growth and development and places a major limit on crop productivity in cultivated areas. Previously, qLTG3-1, a major quantitative trait locus controlling low-temperature tolerance at the germination stage in rice (called low-temperature germinability) was identified, which encodes a protein of unknown function. To identify genes targeted by qLTG3-1, a genome-wide expression profiling analysis using the 44 K Rice Oligo microarray was performed. Because the expression of qLTG3-1 was dramatically increased at 1 day after incubation, the expression profiles at this time were compared between Hayamasari, which has a loss-of-function qLTG3-1 allele, and a near isogenic line with a functional allele. A total of 4,587 genes showed significant differences between their expression levels in the two lines. Most of these genes might be involved in the process of seed germination itself, and then a focus was made on qLTG3-1 dependently induced or suppressed genes, defined as 'qLTG3-1 dependent' genes. Twenty-nine 'qLTG3-1 dependent' genes with diverse functions were categorized, implying that disruption of cellular homeostasis leads to a wide range of metabolic alterations and diverse cross-talk between various signaling pathways. In particular, genes involved in defense responses were up-regulated by qLTG3-1, indicating that qLTG3-1 expression is required for the expression of defense response genes in low-temperature germinability in rice.

Molecular identification of a major quantitative trait locus, qLTG3–1 , controlling low-temperature germinability in rice

Tolerance to abiotic stress is an important agronomic trait in crops and is controlled by many genes, which are called quantitative trait loci (QTLs). Identification of these QTLs will contribute not only to the understanding of plant biology but also for plant breeding, to achieve stable crop production around the world. Previously, we mapped three QTLs controlling low-temperature tolerance at the germination stage (called low-temperature germinability). To understand the molecular basis of one of these QTLs, qLTG3-1 (quantitative trait locus for low-temperature germinability on chromosome 3), map-based cloning was performed, and this QTL was shown to be encoded by a protein of unknown function. The QTL qLTG3-1 is strongly expressed in the embryo during seed germination. Before and during seed germination, specific localization of beta-glucuronidase staining in the tissues covering the embryo, which involved the epiblast covering the coleoptile and the aleurone layer of the seed coat, was observed. Expression of qLTG3-1 was tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. These phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.

QTL and Epistasis for Low Temperature Germinability in Rice

QTL and Epistasis for Low Temperature Germinability in Rice

QTL and Epistasis for Low Temperature Germinability in Rice

A high germination rate at a relatively low temperature is essential for direct seeding rice varieties. The objectives of this study were to detect quantitative trait loci (QTLs) associated with low temperature germinability (LTG) and analyze their epistasis effects. A total of 81 recombinant inbred lines (RILs), derived from a cross between varieties Kinmaze ( japonica) and DV85 ( indica), was used for QTL mapping in 3 environments, i.e., Nanjing, Jiangsu Province in 2002 and 2003, and Lingshui, Hainan Province in 2002. The germination rate at 15°C, after a 10-day germination culture, was taken as an LTG indicator. A total of 11 QTLs on chromosomes 2, 5, 7, 8, 11, and 12 were detected in the 3 environments by QTL Mapping 2.0 software including the 2 QTLs mapped in similar genomic regions in all the enviroments. The 2 QTLs were located on chromosomes 7 and 11 and origniated from Kinmaze and DV85 each. The maximum percentages of phenotypic variation explained (PVE) of the 2 QTLs were both 27.9%. Epistatic interaction analysis showed slightly low PVE of the 2 QTLs.

イタリア由来イネ系統「Italica Livorno」を用いたイネ低温発芽性遺伝子の単離

イタリア由来イネ系統「Italica Livorno」を用いたイネ低温発芽性遺伝子の単離

A major gene for low temperature germinability in rice (Oryza sativa L.)

Low temperature-induced retardation of seedling growth is a common problem in temperate rice-growing areas, at high altitudes of tropical and sub-tropical areas, and in areas with a cold irrigation water supply. Studies on low temperature germinability have revealed complex inheritance of the trait. The purpose of this study was to identify the gene(s) for low temperature germinability using Italica Livorno as a donor parent. The frequency distributions for the germination rate at 15 °C in the F2 and BC1F1 populations showed continuous segregation, suggesting that low temperature germinability was under polygenic control. Since some lines in the BC1F1 population showed vigorous low temperature germinability similar to that of Italica Livorno, backcrosses until the BC5F1 generation was carried out using Hayamasari as the recurrent parent. Clear segregations of low temperature germinability were observed in the BC5F1 and BC5F2 populations. The distribution of low temperature germinability fitted a single-gene segregation, indicating that a single dominant gene with a large effect was transferred to Hayamasari. This gene is tentatively symbolized as Ltg(t). Low temperature germinability of near isogenic lines for Ltg(t) was similar to that of Italica Livorno. Ltg(t) should greatly contribute to the improvement and manipulation of low temperature germinability in rice breeding programs.

Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.).

Low-temperature germination is one of the major determinants for stable stand establishment in the direct seeding method in temperate regions, and at high altitudes of tropical regions. Quantitative trait loci (QTLs) controlling low-temperature germinability in rice were identified using 122 backcross inbred lines (BILs) derived from a cross between temperate japonica varieties, Italica Livorno and Hayamasari. The germination rate at 15 degrees C was measured to represent low-temperature germination and used for QTL analysis. The germination rate at 15 degrees C for 7 days of Italica Livorno and Hayamasari was 98.7 and 26.8%, respectively, and that of BILs ranged from 0 to 83.3%. Using restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers, we constructed a linkage map which corresponded to about 90% of the rice genome. Three putative QTLs associated with low-temperature germination were detected. The most effective QTL, qLTG-3-1 on chromosome 3, accounted for 35.0% of the total phenotypic variation for low-temperature germinability. Two additional QTLs, qLTG-3-2 on chromosome 3 and qLTG-4 on chromosome 4, were detected and accounted for 17.4 and 5.5% of the total phenotypic variation, respectively. The Italica Livorno alleles in all detected QTLs increased the low-temperature germination rate.