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.     

Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars

Backcrossed inbred lines (BILs) and a set of reciprocal chromosome segment substitution lines (CSSLs) derived from crosses between japonica rice cultivars Nipponbare and Koshihikari were used to detect quantitative trait loci (QTLs) for pre-harvest sprouting resistance. In the BILs, we detected one QTL on chromosome 3 and one QTL on chromosome 12. The QTL on the short arm of chromosome 3 accounted for 45.0% of the phenotypic variance and the Nipponbare allele of the QTL increased germination percentage by 21.3%. In the CSSLs, we detected seven QTLs, which were located on chromosomes 2, 3 (two), 5, 8 and 11 (two). All Nipponbare alleles of the QTLs were associated with an increased rate of germination. The major QTL for pre-harvest sprouting resistance on the short arm of chromosome 3 was localized to a 474-kbp region in the Nipponbare genome by the SSR markers RM14240 and RM14275 by using 11 substitution lines to replace the different short chromosome segments on chromosome 3. This QTL co-localized with the low-temperature germinability gene qLTG3-1. The level of germinability under low temperature strongly correlated with the level of pre-harvest sprouting resistance in the substitution lines. Sequence analyses revealed a novel functional allele of qLTG3-1 in Nipponbare and a loss-of-function allele in Koshihikari. The allelic difference in qLTG3-1 between Nipponbare and Koshihikari is likely to be associated with differences in both pre-harvest sprouting resistance and low-temperature germinability.     

Mapping of quantitative trait loci controlling low-temperature germinability in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> 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°C was measured to represent low-temperature germination and used for QTL analysis. The germination rate at 15°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.Communicated by F. Salamini     

Detection of quantitative trait loci controlling extremely early heading in rice

To clarify the genetic basis of extremely early heading in rice, we conducted quantitative trait locus (QTL) analyses using F₂ populations from two genetically wide cross combinations, Hayamasari/Kasalath (HaF₂) and Hoshinoyume/Kasalath (HoF₂). Hayamasari and Hoshinoyume are extremely early-heading japonica cultivars. Photoperiod sensitivity is completely lost in Hayamasari and weak in Hoshinoyume. Three QTLs, QTL(chr6), QTL(chr7), and QTL(chr8), for days-to-heading (DTH) in HaF₂ were detected on chromosomes 6, 7, and 8, respectively, and QTL(chr6) and QTL(chr7) were detected in HoF₂. On the basis of the chromosomal locations, QTL(chr6), QTL(chr7), and QTL(chr8) may be likely to be Hd1, Hd4, and Hd5, respectively, which had been detected previously as QTLs for DTH in an F₂ population of Nipponbare × Kasalath. Alleles of QTL(chr7) decreased DTH dramatically in both Hayamasari and Hoshinoyume, suggesting that QTL(chr7) has a major role in determining extremely early heading. In addition, allele-specific interactions were detected between QTL(chr6), QTL(chr7) and QTL(chr8). This result suggests that not only allelic differences but also epistatic interactions contribute to extremely early heading. QTL(chr8) was detected in HaF₂, but not in HoF₂, suggesting that it determines the difference in DTH between Hayamasari and Hoshinoyume. A major QTL was also detected in the region of QTL(chr8) in QTL analysis using an F₂ population of Hayamasari × Hoshinoyume. This result supports the idea that QTL(chr8) is a major factor that determines the difference in DTH between Hayamasari and Hoshinoyume, and is involved in photoperiod sensitivity.     

Selection for low-temperature germinability on the short arm of chromosome 3 in rice cultivars adapted to Hokkaido,Japan

In plant breeding with intensive selection, the haplotype patterns in the targeted chromosomal regions may become monogenic among local populations with the most desirable combination of loci. This study demonstrated that the chromosomal region surrounding qLTG3-1 was under selection during rice breeding programs in a local region of Japan, Hokkaido. qLTG3-1 is a major quantitative trait loci controlling tolerance to low-temperature at the seed germination stage in rice, termed low-temperature germinability. A clear association between qLTG3-1 alleles and low-temperature germinability was detected among 64 rice cultivars from Hokkaido. The allele with a loss-of-function mutation seemed to be selected during rice breeding programs. Comparison of haplotype patterns along with the short arm of chromosome 3 revealed that the selection of qLTG3-1 alleles was focused on a distinct chromosomal region of at most 130 kb. In the short arm of chromosome 3, two major traits associated with the adaptability to local conditions have been identified; eating quality and heading date. This study demonstrated that recombinant haplotype patterns for these traits might shape the adaptability to local environmental conditions and market demands during rice breeding programs in addition to the selection of qLTG3-1 alleles. The present results provide new opportunities for the design of hybridization combinations based on the haplotype patterns of chromosomal regions under selection during rice breeding programs in local regions.     

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.     

Genetic interactions involved in the inhibition of heading by heading date QTL, <Emphasis Type="Italic">Hd2</Emphasis> in rice under long-day conditions

Heading date is the one of the most important traits in rice breeding, because it defines where rice can be cultivated and influences the expression of various agronomic traits. To examine the inhibition of heading by Heading date 2 (Hd2), previously detected on the distal end of chromosome 7’s long arm by quantitative trait locus (QTL) analysis, we developed backcross inbred lines (BILs) from Koshihikari, a leading Japanese cultivar, and Hayamasari, an extremely early heading cultivar. The BILs were cultivated under natural field conditions in Tsukuba Japan, and under long-day (14.5 h), extremely long-day (18 h), and short-day (10 h) conditions. Combinations of several QTLs near Hd1, Hd2, Ghd7, Hd5, and Hd16 were detected under these four conditions. Analysis of advanced backcross progenies revealed genetic interactions between Hd2 and Hd16 and between Hd2 and Ghd7. In the homozygous Koshihikari genetic background at Hd16, inhibition of heading by the Koshihikari allele at Hd2 was smaller than that with the Hayamasari Hd16 allele. Similarly, in the homozygous Koshihikari genetic background at Ghd7, the difference in heading date caused by different alleles at Hd2 was smaller than in plants homozygous for the Hayamasari Ghd7 allele. Based on these results, we conclude that Hd2 and its genetic interactions play an important role in controlling heading under long-day conditions. In addition, QTLs near Hd2, Hd16, and Ghd7, which are involved in inhibition of heading under long-day conditions, function in the same pathway that controls heading date.     

QTL editing confers opposing yield performance in different rice varieties

Grain yield is one of the most important and complex trait for genetic improvement in crops; it is known to be controlled by a number of genes known as quantitative trait loci(QTLs). In the past decade, many yield-contributing QTLs have been identified in crops.However, it remains unclear whether those QTLs confer the same yield performance in different genetic backgrounds. Here, we performed CRISPR/Cas_9-mediated QTL editing in five widely-cultivated rice varieties and revealed that the same QTL can have diverse, even opposing, effects on grain yield in different genetic backgrounds.     

Genetic dissection of grain traits in Yamadanishiki,an excellent sake-brewing rice cultivar

Key message

The grain traits of Yamadanishiki, an excellent sake-brewing rice cultivar in Japan, are governed by multiple QTLs, namely, a total of 42 QTLs including six major QTLs.

Abstract

Japanese rice wine (sake) is produced using brewing rice (Oryza sativa L.) that carries traits desirable for sake-brewing, such as a larger grain size and higher white-core expression rate (WCE) compared to cooking rice cultivars. However, the genetic basis for these traits in brewing rice cultivars is still unclear. We performed analyses of quantitative trait locus (QTL) of grain and days to heading over 3 years on populations derived from crosses between Koshihikari, a cooking rice, and Yamadanishiki, an excellent sake-brewing rice. A total of 42 QTLs were detected for the grain traits, and the Yamadanishiki alleles at 16 QTLs contributed to larger grain size. Two major QTLs essential for regulating both 100-grain weight (GWt) and grain width (GWh) were harbored in the same regions on chromosomes 5 and 10. An interaction was noted between the environment and the QTL associated with WCE on chromosome 6, which was detected in two of 3 years. In addition, two QTLs for WCE on chromosomes 3 and 10 overlapped with the QTLs for GWt and GWh, suggesting that QTLs associated with grain size also play an important role in the formation of white-core. Despite differences in the rate of grain growth in both Koshihikari and Yamadanishiki across 2 years, the WCE in Yamadanishiki remained consistent, thus demonstrating that the formation of white-core does not depend on grain filling speed. These data can be informative for programs involved in breeding better cooking and brewing rice cultivars.

     

QTL mapping of combining ability and heterosis of agronomic traits in rice backcross recombinant inbred lines and hybrid crosses

Background

Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis.

Methodology/Principal Findings

In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits.

Conclusions/Significance

The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1–6 in this study) were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability.     

Association Mapping and Validation of QTLs for Flour Yield in the Soft Winter Wheat Variety Kitahonami

The winter wheat variety Kitahonami shows a superior flour yield in comparison to other Japanese soft wheat varieties. To map the quantitative trait loci (QTL) associated with this trait, association mapping was performed using a panel of lines from Kitahonami’s pedigree, along with leading Japanese varieties and advanced breeding lines. Using a mixed linear model corrected for kernel types and familial relatedness, 62 marker-trait associations for flour yield were identified and classified into 21 QTLs. In eighteen of these, Kitahonami alleles showed positive effects. Pedigree analysis demonstrated that a continuous pyramiding of QTLs had occurred throughout the breeding history of Kitahonami. Linkage analyses using three sets of doubled haploid populations from crosses in which Kitahonami was used as a parent were performed, leading to the validation of five of the eight QTLs tested. Among these, QTLs on chromosomes 3B and 7A showed highly significant and consistent effects across the three populations. This study shows that pedigree-based association mapping using breeding materials can be a useful method for QTL identification at the early stages of breeding programs.     

Shaping melons: agronomic and genetic characterization of QTLs that modify melon fruit morphology

The consistency of quantitative trait locus (QTL) effects among genetic backgrounds is a key factor for introgressing QTLs from initial mapping experiments into applied breeding programs. We have selected four QTLs (fs6.4, fw4.3, fw4.4 and fw8.1) involved in melon fruit morphology that had previously been detected in a collection of introgression lines derived from the cross between a Spanish cultivar, “Piel de Sapo,” and the Korean accession PI161375 (Songwan Charmi). Introgression lines harboring these QTLs were crossed with an array of melon inbred lines representative of the most important cultivar types. Hybrids of the introgression and inbred lines, with the appropriate controls, were evaluated in replicated agronomic trials. The effects of the QTLs were consistent among the different genetic backgrounds, demonstrating the utility of these QTLs for applied breeding programs in modifying melon fruit morphology. Three QTLs, fw4.4, fs6.4 and fs12.1 were subjected to further study in order to map them more accurately by substitution mapping using a new set of introgression lines with recombination events within the QTL chromosome region. The position of the QTLs was narrowed down to 36–5 cM, depending on the QTL. The results presented in the current study set the basis for the use of these QTLs in applied breeding programs and for the molecular characterization of the genes underlying them.     

Transmission of important chromosomal regions under selection revealed in rice pedigree breeding programs

Genetic analysis across a whole plant genome based on pedigree information offers considerable potential for enhancing genetic gain from plant breeding programs through quantitative trait loci (QTL) mapping and marker-assisted selection. Here, we report its application for graphically genotyping varieties used in Chinese japonica rice (Oryza sativa L.) pedigree breeding programs. We identified 34 important chromosomal regions from the founder parent that are under selection in the breeding programs, and by comparing donor genomic regions that are under selection with QTL locations of agronomic traits, we found that QTL clustered in important genomic regions, in accordance with association analyses of natural populations and other previous studies. The convergence of genomic regions under selection with QTL locations suggests that donor genomic regions harboring key genes/QTL for important agronomic traits have been selected by plant breeders since the 1950s from the founder rice plants. The results provide better understanding of the effects of selection in breeding programs on the traits of rice cultivars. They also provide potentially valuable information for enhancing rice breeding programs through screening candidate parents for targeted molecular markers, improving crop yield potential and identifying suitable genetic material for use in future breeding programs.     

Identification of qRBS1, a QTL involved in resistance to bacterial seedling rot in rice

Bacterial seedling rot (BSR), a destructive disease of rice (Oryza sativa L.), is caused by the bacterial pathogen Burkholderia glumae. To identify QTLs for resistance to BSR, we conducted a QTL analysis using chromosome segment substitution lines (CSSLs) derived from a cross between Nona Bokra (resistant) and Koshihikari (susceptible). Comparison of the levels of BSR in the CSSLs and their recurrent parent, Koshihikari, revealed that a region on chromosome 10 was associated with resistance. Further genetic analyses using an F₅ population derived from a cross between a resistant CSSL and Koshihikari confirmed that a QTL for BSR resistance was located on the short arm of chromosome 10. The Nona Bokra allele was associated with resistance to BSR. Substitution mapping in the Koshihikari genetic background demonstrated that the QTL, here designated as qRBS1 (quantitative trait locus for RESISTANCE TO BACTERIAL SEEDLING ROT 1), was located in a 393-kb interval (based on the Nipponbare reference genome sequence) defined by simple sequence repeat markers RM24930 and RM24944.     

QTL analysis of percentage of grains with chalkiness in Japonica rice (Oryza sativa)

Appearance quality of rice grains is a major problem for rice production in many areas of the world. We conducted a molecular marker-based genetic analysis of percentage of grains with chalkiness (PGWC), which is a determining factor for appearance quality; it strongly affects milling, eating and cooking quality. An F(8) recombinant inbred line population, which consists of 261 lines derived from a cross between Koshihikari (Japonica) and C602 (Japonica), was used for QTL mapping. Three QTLs related to PGWC were detected on chromosomes 5, 8 and 10, together explaining 50.8% of the genetic variation. The 'Koshihikari' alleles qJPGC-5, qJPGC-8 and the 'C602' alleles at qJPGC-10 were associated with reduced PGWC. The QTL contributions to phenotypic variance were 18.2, 9.6 and 25%, respectively. These QTL markers for PGWC could be used for developing improved varieties.     

Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application

The major quantitative trait locus (QTL) Phosphorus uptake1 (Pup1) confers tolerance of phosphorus deficiency in soil and is currently one of the most promising QTLs for the development of tolerant rice (Oryza sativa) varieties. To facilitate targeted introgression of Pup1 into intolerant varieties, the gene models predicted in the Pup1 region in the donor variety Kasalath were used to develop gene-based molecular markers that are evenly distributed over the fine-mapped 278-kb QTL region. To validate the gene models and optimize the markers, gene expression analyses and partial allelic sequencing were conducted. The markers were tested in more than 80 diverse rice accessions revealing three main groups with different Pup1 allele constitution. Accessions with tolerant (group I) and intolerant (group III) Pup1 alleles were distinguished from genotypes with Kasalath alleles at some of the analyzed loci (partial Pup1; group II). A germplasm survey additionally confirmed earlier data showing that Pup1 is largely absent from irrigated rice varieties but conserved in varieties and breeding lines adapted to drought-prone environments. A core set of Pup1 markers has been defined, and sequence polymorphisms suitable for single-nucleotide polymorphism marker development for high-throughput genotyping were identified. Following a marker-assisted backcrossing approach, Pup1 was introgressed into two irrigated rice varieties and three Indonesian upland varieties. First phenotypic evaluations of the introgression lines suggest that Pup1 is effective in different genetic backgrounds and environments and that it has the potential to significantly enhance grain yield under field conditions.     

基于CSSL的水稻抽穗期QTL定位及遗传分析

抽穗期是水稻（Oryza sativa）品种的重要农艺性状之一,适宜的抽穗期是获得理想产量的前提。鉴定和定位水稻抽穗期基因/QTL,分析其遗传效应对改良水稻抽穗期至关重要。以籼稻品种9311（Oryzasativa ssp.indica‘Yangdao 6’）为受体,粳稻品种日本晴（Oryza sativa ssp.japonica‘Nipponbare’）为供体构建的94个染色体片段置换系群体为材料,以P≤0.01为阈值,对置换片段上的抽穗期QTL进行了鉴定。采用代换作图法共定位了4个控制水稻抽穗期的QTL,分别位于第3、第4、第5和第8染色体;QTL的加性效应值变化范围为–6.4––2.7,加性效应百分率变化范围为–6.4%––2.7%;qHD-3和qHD-8加性效应值较大,表现主效基因特征。为了进一步定位qHD-3和qHD-8,在目标区域加密16对SSR引物,qHD-3和qHD-8分别被界定在第3染色体RM3166–RM16206之间及第8染色体RM4085–RM8271之间,其遗传距离分别为13.9cM和6.4cM。研究结果为利用分子标记辅助选择改良水稻抽穗期奠定了基础。     

Efficacy of microarray profiling data combined with QTL mapping for the identification of a QTL gene controlling the initial growth rate in rice

Seedling vigor, which is controlled by many quantitative trait loci (QTLs), is one of several important agronomic traits for direct-seedling rice systems. However, isolating these QTL genes is laborious and expensive. Here, we combined QTL mapping and microarray profiling to identify QTL genes for seedling vigor. By performing QTL mapping using 82 backcross inbred lines (BILs) of the Koshihikari (japonica) and Habataki (indica) cultivars for the rice initial growth, we identified two QTLs, early-stage plant development1/2 (qEPD1 and qEPD2), whose Koshihikari alleles promote plant height and/or leaf sheath length. Phenotypic analysis of the two substituted lines carrying the Habataki qEPD1 or qEPD2 allele revealed that qEPD2 functioned more dominantly for the initial growth of rice. From the microarray experiment, 55 and 45 candidate genes were found in the qEPD1 and qEPD2 genomic regions, which are expressed differentially between each substitution line (SL) and Koshihikari. Gibberellin 20 oxidase-2 (OsGA20ox2), which is identical to Semi Dwarf1 (SD1), was included among the 55 candidate genes of qEPD1, whereas its paralog, OsGA20ox1, was included among the 45 candidate genes of qEPD2. Consistently, introduction of the Koshihikari OsGA20ox1 allele into SL(qEPD2) increaseed its plant height and leaf sheath length significantly relative to the introduction of the Habataki OsGA20ox1 allele. Therefore, microarray profiling could be useful for rapidly screening QTL candidate genes. We concluded that OsGA20ox1 and OsGA20ox2 (SD1) function during the initial growth of rice, but OsGA20ox1 plays a dominant role in increasing plant height and leaf sheath length at the initial growth stage.     

水稻蒸煮品质相关QTL定位及候选基因分析

挖掘与稻米蒸煮品质相关的数量性状基因座(quantitative trait locus, QTL)，分析候选基因，并通过遗传育种手段改良稻米蒸煮品质相关性状，可有效提升稻米的口感。以籼稻华占(Huazhan, HZ)、粳稻热研2号(Nekken2)及由其构建的120个重组自交系(recombinant inbred lines, RILs)群体为实验材料，测定成熟期稻米的糊化温度(gelatinization temperature, GT)、胶稠度(gel consistency, GC)和直链淀粉含量(amylose content, AC)。结合高密度分子遗传图谱进行QTL定位，共检测到26个与稻米蒸煮品质相关的QTLs (糊化温度相关位点1个、胶稠度相关位点13个、直链淀粉含量相关位点12个)，其中最高奇数的可能性(likelihood of odd, LOD)值达30.24。通过实时荧光定量PCR (quantitative real-time polymerase chain reaction, qRT-PCR)分析定位区间内候选基因的表达量，发现6个基因在双亲间的表达量差异显著，推测LOC_Os04g20270和LOC_Os11g40100的高表达可能会极大地提高稻米的胶稠度，而LOC_Os01g04920和LOC_Os02g17500的高表达以及LOC_Os03g02650和LOC_Os05g25840的低表达有助于降低直链淀粉含量。这些结果为培育优质水稻新品种奠定了分子基础，并为揭示稻米蒸煮品质的分子调控机制提供了重要的遗传资源。     

Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice

Seed vigor is an index of seed quality that is used to describe the rapid and uniform germination and the establishment of strong seedlings in any environmental conditions.Strong seed vigor in low-temperature germination conditions is particularly important in direct-sowing rice production systems. However, seed vigor has not been selected as an important breeding trait in traditional breeding programs due to its quantitative inherence. In this study, we identified and mapped eight quantitative trait loci(QTLs) for seed vigor by using a recombinant inbred population from a cross between rice(Oryza sativa L. ssp. indica) cultivars ZS97 and MH63.Conditional QTL analysis identified qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-11 influenced seedling establishment and that qSV-5a, qSV-5c, and qSV-8 influenced only germination. Of these,qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-8 were low-temperature-specific QTLs. Two major-effective QTLs, qSV-1, and qSV-5c were narrowed down to 1.13-Mbp and 400-kbp genomic regions, respectively. The results provide tightly linked DNA markers for the marker-assistant pyramiding of multiple positive alleles for increased seed vigor in both normal and low-temperature germination environments.