Quantitative trait loci controlling aluminium tolerance in two accessions of Arabidopsis thaliana (Landsberg erecta and Cape Verde Islands)

Quantitative trait loci (QTL) analysis of aluminium (Al) tolerance was performed using Ler/Cvi recombinant inbred (RI) lines of Arabidopsis thaliana. Relative root length (RRL) (root length with 4 µm Al/root length with no Al at pH 5.0) on day 5 was used as the Al tolerance index for QTL analysis. Al tolerance judged by RRL was well correlated to tolerance judged by other indexes, including accumulation of callose, reactive oxygen species in the root apex and growth performance on acid soil containing a large amount of exchangeable Al. Using data sets with an h_b² of 0.91, two QTLs were detected at the top of chromosome 1 and bottom of chromosome 3. These QTLs explained 40 and 16% of the phenotypic variation of Al tolerance, respectively, and the positive effect of the Cvi allele. The QTL on chromosome 1 overlapped with a major QTL in another recombinant inbred population, and is possibly related to malate excretion. A complete pair-wise search revealed 11 sets of epistatic interacting loci pairs, which accounted for the transgressive segregation among the RI population. Several epistatic interactions shared the same chromosomal region, indicating the possible involvement of regulatory proteins in Al tolerance in Arabidopsis.     

Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, <Emphasis Type="SmallCaps">ORYZA RUFIPOGON</Emphasis> Griff., into indica rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

This study was conducted to identify and map the quantitative trait locus (QTL) controlling Al tolerance in rice using molecular markers. A population of 171 F(6) recombinant inbred lines (RILs) derived from the cross of Oryza sativa (IR64), the Al susceptible parent, and Oryza rufipogon, the Al tolerant parent, was evaluated for Al tolerance using a nutrient solution with and without 40 ppm of active Al(+3). A genetic map, consisting of 151 molecular markers covering 1,755 cM with an average distance of 11.6 cM between loci, was constructed. Nine QTLs were dentified including one for root length under non-stress conditions (CRL), three for root length under Al stress (SRL) and five for relative root length (RRL). O. rufipogon contributed favorable alleles for each of the five QTLs for RRL, which is a primary parameter for Al tolerance, and individually they explained 9.0-24.9% of the phenotypic variation. Epistatic analysis revealed that CRL was conditioned by an epistatic effect, whereas SRL and RRL were controlled by additive effects. Comparative genetic analysis showed that QTLs for RRL, which mapped on chromosomes 1 and 9, appear to be consistent among different rice populations. Interestingly, a major QTL for RRL, which explained 24.9% of the phenotypic variation, was found on chromosome 3 of rice, which is conserved across cereal species. These results indicate the possibilities to use marker-assisted selection and pyramiding QTLs for enhancing Al tolerance in rice. Positional cloning of such QTLs introgressed from O. rufipogon will provide a better understanding of the Al tolerance mechanism in rice and the evolutionary genetics of plant adaptation to acid-soil conditions across cereal species.     

QTL analysis of Al tolerance in recombinant inbred lines of Arabidopsis thaliana

Quantitative trait loci (QTLs) and epistasis for Arabidopsis thaliana aluminum (Al) tolerance were analyzed using a recombinant inbred (RI) population of 100 lines derived from a cross between Landsberg erecta and Columbia (Col). Root growth of the RI population was determined in hydroponics using solutions containing 0 or 4 micro M of AlCl(3 )and a series of nutrients, except P(i), at pH 5.0. Al tolerance was defined as relative root length [RRL: plus Al/minus Al (%)], and the RI lines ranged from 22.6 to 97.4% with a broad sense heritability of 0.99. Using the composite interval mapping method, two significant single factor QTLs (P<0.05) were detected by RRL on chromosomes 1 and 4, where the Col allele showed positive and negative effects on the Al tolerance. These QTLs could explain about 43% of the total variation of Al tolerance among the RI population. On the other hand, five epistatic loci pairs were identified by the complete pair-wise search method (P<0.0005). No single factor QTL and epistatic loci pairs were shared by the root length in the control and the RRL, suggesting that the loci identified by the RRL would be specific for Al treatment and controlling Al tolerance among the RI population.     

QTLs and epistasis for seminal root length under a different water supply in rice (Oryza sativa L.)

To identify the genetic background of seminal root length under different water-supply conditions, a recombinant inbred (RI) population consisting of 150 lines, derived from a cross between an indica lowland rice, IR1552, and a tropical japonica upland rice, Azucena, was used in both solution culture (lowland condition) and paper culture (upland condition). Quantitative trait loci (QTLs) and epistatic loci for seminal root length were analyzed using 103 restriction fragment length polymorphism (RFLP) markers and 104 amplified fragment length polymorphism (AFLP) markers mapped on 12 chromosomes based on the RI population. One QTL for seminal root length in solution culture (SRLS) and one for seminal root length in paper culture (SRLP) were detected on chromosomes 8 and 1, and about 11% and 10% of total phenotypic variation were explained, respectively. The QTL for SRLP on chromosome 1 was very similar with the QTL for the longest nodal root referred to in a previous report; this QTL may be phenotypically selectable in a breeding program using paper culture. Five pairs of epistatic loci for SRLS were detected, but only one for SRLP, which accounted for about 60% and 20% of the total variation in SRLS and SRLP, respectively. The results indicate that epistasis is a major genetic basis for seminal root length, and there is a different genetic system responsible for seminal root growth under different water supply conditions. Received: 26 May 2000 / Accepted: 19 October 2000     

Mapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations

To investigate the genetic factors underlying constitutive and adaptive morphological traits of roots under different water-supply conditions, a recombinant inbred line (RIL) population derived from a cross between the lowland rice variety IR1552 and the upland rice variety Azucena with 249 molecular markers, was used in cylindrical-pot experiments. Eighteen QTLs were detected for seminal root length (SRL), adventitious root number (ARN), and lateral root length (LRL) and lateral root number (LRN) on the seminal root at a soil depth of from 3 to 6 cm under flooding and upland conditions. One identical QTL was detected under both flooding and upland conditions. The relative parameters under the two water-supply conditions were also used for QTL analysis. Five QTLs for upland induced variations in the traits were detected with the positive alleles from Azucena. A comparative analysis was performed for the QTLs detected in this study and those reported from two other populations with Azucena as a parent. Several identical QTLs for root elongation were found across the three populations with positive alleles from Azucena. Candidate genes were screened from ESTs and cDNA-AFLP clones for comparative mapping with the detected QTLs. Two genes for cell expansion, OsEXP2 and endo-1,4--D-glucanase EGase, and four cDNA-AFLP clones from root tissues of Azucena, were mapped on the intervals carrying the QTLs for SRL and LRL under upland conditions, respectively.Communicated by H.C. Becker     

Impact of epistasis and QTL×environment interaction on the developmental behavior of plant height in rice (Oryza sativa L.)

QTLs with epistatic effects and environmental interaction effects for the developmental behavior of plant height in rice were studied by conventional and conditional methods for quantitative trait loci (QTLs) by mapping with a doubled-haploid population of 123 lines from IR64/Azucena in three environments. The results showed that epistatic effects were important and most epistasis could be detected only by conditional QTL mapping, while most non–epistatic QTLs could be detected by both conventional and conditional methods. Many modificative QTLs showed only epistatic effects without their own additive effects at some stages. QTL×environment (QE) interaction effects were detected more often than QTL main effects for plant-height behavior, which might indicate that gene expression could be greatly affected by the environment. No QTLs had effects during the whole of ontogeny. Conditional QTL mapping might be a valid way to reveal dynamic gene expression for the development of quantitative traits, especially for epistatic effects. Received: 19 May 2000 / Accepted: 27 October 2000     

Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety

A marker-assisted back-crossing (MABC) breeding programme was conducted to improve the root morphological traits, and thereby drought tolerance, of the Indian upland rice variety, Kalinga III. This variety, the recurrent parent in the MABC, had not previously been used for quantitative trait locus (QTL) mapping. The donor parent was Azucena, an upland japonica variety from Philippines. Five segments on different chromosomes were targeted for introgression; four segments carried QTLs for improved root morphological traits (root length and thickness) and the fifth carried a recessive QTL for aroma. Some selection was made at non-target regions for recurrent parent alleles. We describe the selection made in three backcross (BC) generations and two further crosses between BC₃ lines to pyramid (stack) all five target segments. Pyramids with four root QTLs were obtained in eight generations, completed in 6 years using 3,000 marker assays in a total of 323 lines. Twenty-two near-isogenic lines (NILs) were evaluated for root traits in five field experiments in Bangalore, India. The target segment on chromosome 9 (RM242-RM201) significantly increased root length under both irrigated and drought stress treatments, confirming that this root length QTL from Azucena functions in a novel genetic background. No significant effects on root length were found at the other four targets. Azucena alleles at the locus RM248 (below the target root QTL on chromosome 7) delayed flowering. Selection for the recurrent parent allele at this locus produced early-flowering NILs that were suited for upland environments in eastern India.     

不同供水条件下水稻幼苗根系形成的遗传分析

利用分子标记图谱对溶液培养与旱作培养（纸培养）下的水稻（Oryza sativa L.)幼苗的种子根与最长不定根长,不定根数,总根干重,根冠比等性状进行了基因定位与遗传分析。4种参数共检测到6个数量性状位点（quantitative trait loci,QTLs)与22对上位性互作位点,其中溶液培养中的最长不定根长,总根干重和旱作培养中的总根干重检测到的QTLs位点对总变异的贡献率分别为20％,23％和13％左右;旱作培养中的最长不定根长,不定根数,根冠比和溶液培养中的根冠比仅检测到上位性位点,对表型变异的贡献率在12％－61％之间,溶液培养与旱作条件下没有一个或一对检测到的QTL或互作位点完全相同,提示溶液培养和旱作条件下影响幼苗根系生长的遗传机制差异,上位性作用对旱作培养条件下的根生长具重要影响。     

QTL Analysis of Na+ and K+ Concentrations in Roots and Shoots under Different Levels of NaCl Stress in Rice (Oryza sativa L.)

The key to plant survival under NaCl salt stress is maintaining a low Na⁺ level or Na⁺/K⁺ ratio in the cells. A population of recombinant inbred lines (RILs, F_2∶9) derived from a cross between the salt-tolerant japonica rice variety Jiucaiqing and the salt-sensitive indica variety IR26, was used to determine Na⁺ and K⁺ concentrations in the roots and shoots under three different NaCl stress conditions (0, 100 and 120 mM NaCl). A total of nine additive QTLs were identified by QTL Cartographer program using single-environment phenotypic values, whereas eight additive QTLs were identified by QTL IciMapping program. Among these additive QTLs, five were identified by both programs. Epistatic QTLs and QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values, and one additive QTL and nine epistatic QTLs were identified. There were three epistatic QTLs identified for Na⁺ in roots (RNC), three additive QTLs and two epistatic QTLs identified for Na⁺ in shoots (SNC), four additive QTLs identified for K⁺ in roots (RKC), four additive QTLs and three epistatic QTLs identified for K⁺ in shoots (SKC) and one additive QTL and one epistatic QTL for salt tolerance rating (STR). The phenotypic variation explained by each additive, epistatic QTL and QTL×environment interaction ranged from 8.5 to 18.9%, 0.5 to 5.3% and 0.7 to 7.5%, respectively. By comparing the chromosomal positions of these additive QTLs with those previously identified, five additive QTLs, qSNC9, qSKC1, qSKC9, qRKC4 and qSTR7, might represent novel salt tolerance loci. The identification of salt tolerance in selected RILs showed that a major QTL qSNC11 played a significant role in rice salt tolerance, and could be used to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS) approach.     

Genes/QTLs affecting flood tolerance in rice

The adaptation of deepwater rice to flooding is attributed to two mechanisms, submergence tolerance and plant elongation. Using a QTL mapping study with replicated phenotyping under two contrasting (water qualities) submergence treatments and AFLP markers, we were able to identify several genes/QTLs that control plant elongation and submergence tolerance in a recombinant inbred rice population. Our results indicate that segregation of rice plants in their responses to different flooding stress conditions is largely due to the differential expression of a few key elongation and submergence tolerance genes. The most important gene was QIne1 mapped near sd-1 on chromosome 1. The Jalmagna (the deepwater parent) allele at this locus had a very large effect on internal elongation and contributed significantly to submergence tolerance under flooding. The second locus was a major gene, sub1(t), mapped to chromosome 9, which contributed to submergence tolerance only. The third one was a QTL, QIne4, mapped to chromosome 4. The IR74 (non-elongating parent) allele at this locus had a large effect for internal elongation. An additional locus that interacted strongly with both QIne1 and QIne4 appeared near RG403 on chromosome 5, suggesting a complex epistatic relationship among the three loci. Several QTLs with relatively small effects on plant elongation and submergence tolerance were also identified. The genetic aspects of these flooding tolerance QTLs with respect to patterns of differential expression of elongation and submergence tolerance genes under flooding are discussed. Received: 13 December 1999 / Accepted: 14 March 2000<@head-com-p1a.lf>Communicated by G. Wenzel     

Genetic dissection of root growth in rice (Oryza sativa L.). II: mapping quantitative trait loci using molecular markers

Drought is a major abiotic stress of upland rice, and good root growth has been associated with drought avoidance. We report on the genetic mapping of root growth traits in an F₂ population derived from two drought-resistant rice varieties, ‘Bala’ and ‘Azucena’. Restriction fragment length polymorphism (RFLP) between the parents was 32%, and a molecular map with 71 marker loci and 17 linkage groups covering 1280 cM was produced. Quantitative trait loci (QTLs) for eight root growth characteristics were mapped using phenotype data obtained in a hydroponic screen previously described in a companion paper. Using a significance threshold of LOD 2.4, we observed one QTL for maximum root length after 28 days growth on chromosome 11. It had a LOD score of 6.9, explained nearly 30% of the variation and appeared to be largely additive in effect. QTLs for maximum root length after 3, 7, 14 and 21 days of growth were also revealed. Some root-length QTLs, including that on chromosome 11, varied greatly with developmental stage. One QTL for root volume and two QTLs for adventitious root thickness were detected. No QTLs were detected for the length of cells in the mature (fully expanded) zone of adventitious root tips. The results obtained are discussed in the context of previous reports on mapping root growth parameters in rice.     

Effects of genetic background and environment on QTLs and epistasis for rice (Oryza sativa L.) panicle number

A double-haploid (DH) population and a recombinant inbred (RI) line population, derived from a cross between a tropical japonica variety, Azucena, as male parent and two indica varieties, IR64 and IR1552, as female parents respectively, were used in both field and pot experiments for detecting QTLs and epistasis for rice panicle number in different genetic backgrounds and different environments. Panicle number (PN) was measured at maturity. A molecular map with 192 RFLP markers for the DH population and a molecular map with 104 AFLP markers and 103 RFLP markers for the RI population were constructed, in which 70 RFLP markers were the same. Six QTLs were identified in the DH population, including two detected from field experiments and four from pot experiments. The two QTLs, mapped on chromosomes 1 and 12, were identical in both field and pot experiments. In the RI population, nine QTLs were detected, five QTLs from field conditions and four from the pot experiments. Three of these QTLs were identical in both experimental conditions. Only one QTL, linked to CDO344 on chromosome 12, was detected across the populations and experiments. Different epistasitic interaction loci on PN were found under different populations and in different experimental conditions. One locus, flanked by RG323 and RZ801 on chromosome 1, had an additive effect in the DH population, but epistatic effects in the RI population. These results indicate that the effect of genetic background on QTLs is greater than that of environments, and epistasis is more sensitive to genetic background and environments than main-effect QTLs. QTL and epistatic loci could be interchangeable depending on the genetic backgrounds and probably on the environments where they are identified. Received: 26 May 2000 / Accepted: 19 October 2000     

不同遗传背景及环境中水稻（Oryza sativa L.）穗长的QTLs和上位性分析

以粳稻Ａｚｕｃｅｎａ为父本与灿稻ＩＲ６４杂交发展的一双单倍体（ＤＨ） 本,与灿稻ＩＲ１５５２杂交发展的一重组自交系（ＲＩ）群体为材料,应用分子标记图说对２个群体在大田答舅栽２个环境下的穗长进行ＱＴＬｓ及上位性效应分析,ＤＨ群体中共检测６个穗长ＱＴＬｓ,位于第１、４长染色体上的３个ＱＴＬｓ,,在２个环境中稳定表达,未检测一闰性效应,加性效应为穗长遗传主效应,ＲＩ群体中,共检测到３个穗长ＱＴＬｓ及６对     

Genetic Analysis of Root Growth in Rice Seedlings Under Different Water Supply Conditions

To understand the genetic background of root growth of rice (Oryza sativa L.) seedlings under different water supply conditions, quantitative trait loci (QTLs) and epistatic effect on seminal root length, maximum adventitious root length, adventitious root number, total root dry weight and ratio of root to shoot were detected using molecular map including 103 restriction fragment length polymorphism (RFLP) markers and 104 amplified fragment length polymorphism (AFLP) markers mapped on a recombinant inbred line (RIL) population with 150 lines derived from a cross between an lowland rice IR1552 and an upland rice Azucena in both solution culture (lowland condition) and paper culture (upland condition). Six QTLs and twenty-two pairs of epistatic loci for the four parameters were detected. Three QTLs detected for maximum adventitious root length in solution culture (MARLS), total root dry weight in both solution culture and paper culture (TRDWS and TRDWP) accounted for about 20%, 23% and 13% of the total variations, respectively. Only epistatic loci were found for maximum adventitious root length and adventitious root number in paper culture (MARLP and ARNP), and for ratio of root to shoot in both paper and solution culture (R/SP and R/SS), which accounted for about 12%-61% of the total variations in the parameters, respectively. No identical QTL or epistatic loci were found for the parameters in both solution and paper culture. The results indicate that there is a different genetic system responsible to root growth of rice seedlings under lowland and upland conditions and epistasis might be the major genetic basis for MARLP, ARNP, R/SP and R/SS.     

QTL Analysis of Aluminum Resistance in Rice (Oryza sativa L.)

Aluminum (Al) toxicity is considered as one of the primary causes of low-rice productivity in acid soils. In the present study, quantitative trait loci (QTLs) controlling Al resistance based on relative root elongation (RRE) were dissected using a complete linkage map and a recombinant inbred lines (RILs) derived from a cross of Al-tolerant japonica cultivar Asominori (Oryza sativa L.) and Al-sensitive indica cultivar IR24 (O. sativa L.). A total of three QTLs (qRRE-1, qRRE-9, and qRRE-11) were detected on chromosomes 1, 9, and 11 with LOD score ranging from 2.64 to 3.60 and the phenotypic variance explained from 13.5 to 17.7%. The Asominori alleles were all associated with Al resistance at all the three QTLs. The existence of these QTLs was confirmed using Asominori chromosome segment substitution lines (CSSLs) in IR24 genetic background (IAS). By QTL comparative analysis, the two QTLs (qRRE-1and qRRE-9) on chromosomes 1 and 9 appeared to be consistent among different rice populations while qRRE-11 was newly detected and syntenic with a major Al resistance gene on chromosome 10 of maize. This region may provide an important case for isolating genes responsible for different mechanisms of Al resistance among different cereals. These results also provide the possibilities of enhancing Al resistance in rice breeding program by marker-assisted selection (MAS) and pyramiding QTLs.     

水稻耐亚铁毒QTLs的定位

亚铁毒是潜育性水稻土中限制水稻产量的主要因子。利用龙杂8503／IR64的F2和等价的F3群体,在营养液中培养来定位耐亚铁毒的QTLs。通过构建101SSR标记的遗传连锁图谱来确定耐亚铁毒QTLs的位置和特性。借助叶片棕色斑点指数、株高和最大根长3个性状,利用营养液在水稻苗期来评价F2单株、F3群体和亲本龙杂8503、IR64,共检测到叶片棕色斑点指数、株高和最大根长的QTLs20个,分布在水稻的10条染色体上,表明这些性状受多基因控制。控制叶片棕色斑点指数的QTLs分别定位在第1染色体的RM315-RM212、第2染色体的RM6-RM240和第4染色体的RM252-RM451之间。与前人的研究结果比较发现：1）位于第4染色体RM252-RM451之间的控制叶片棕色斑点指数的QTL与水稻功能图谱上控制叶绿素含量减少的QTL的位置一致。另一个位于第1染色体的RM315-RM212之间的控制叶片棕色斑点指数的QTL与水稻功能图谱上位于C178-R2635之间控制叶绿素含量的QTL连锁。2）位于第2染色体RM6-RM240之间的第3个控制叶片棕色斑点指数的QTL与位于RZ58-CD0686的控制钾吸收的QTL连锁。     

QTL × N-level interaction for plant height in rice (Oriza Sativa L.)

Quantitative trait loci (QTLs) for plant height in rice were mapped onto the molecular marker linkage map of a double-haploid (DH) population derived from a cross between IR64 and Azucena under low and high N levels, in both nutrient solution and soil culture experiments. Two QTLs, one on chromosome 1 and the other on chromosome 8, were detected at high N levels in soil and/or nutrient solution culture experiments. A total of 8 QTLs were identified at low N level in the soil and/or nutrient solution culture experiments, which located on chromosomes 1, 2, 3, 4, 5 and 6, respectively. The QTL flanked by the molecular markers RZ730 RZ801 on chromosome 1 was identified in all experimental conditions. This position corresponds to sd-1, a semi-dwarfing gene. The QTLs on chromosomes 2, 3, 4, 5 and 6 were only detected at low N level and the QTL on chromosome 8 was only detected at high N level in the nutrient solution culture experiment. Based on the differing responses to low N stress between two parents and the QTL×N-level interaction observed in this study, it is suggested that the expression of several QTLs associated with plant height could be induced by low N stress.     

QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice

Field resistance is defined as the resistance that allows effective control of a parasite under natural field conditions and is durable when exposed to new races of that parasite. To identify the genes for field resistance to rice blast, quantitative trait loci (QTLs) conferring field resistance to rice blast in Japanese upland rice were detected and mapped using RFLP and SSR markers. QTL analysis was carried out in F₄ progeny lines from the cross between Nipponbare (moderately susceptible, lowland) and Owarihatamochi (resistant, upland). Two QTLs were detected on chromosome 4 and one QTL was detected on each of chromosomes 9 and 12. The phenotypic variation explained by each QTL ranged from 7.9 to 45.7% and the four QTLs explained 66.3% of the total phenotypic variation. Backcrossed progeny lines were developed to transfer the QTL with largest effect using the susceptible cultivar Aichiasahi as a recurrent parent. Among 82 F₃ lines derived from the backcross, resistance segregated in the expected ratio of resistant 1 : heterozygous 2 : susceptible 1. The average score for blast resistance measured in the field was 4.2 ± 0.67, 7.5 ± 0.51and 8.2 ± 0.66, for resistant, heterozygous and susceptible groups, respectively. The resistance gene, designated pi21, was mapped on chromosome 4 as a single recessive gene between RFLP marker loci G271 and G317 at a distance of 5.0 cM and 8.5 cM, respectively. The relationship to previously reported major genes and QTLs conferring resistance to blasts, and the significance of marker-assisted selection to improve field resistance, are discussed. Received: 8 June 2000 / Accepted: 24 November 2000     

Comparison of QTLs for rice seedling morphology under different water supply conditions

The variation of seedling characteristics under different water supply conditions is strongly associated with drought resistance in rice (Oryza sativa L.) and a better elucidation of its genetics is helpful for improving rice drought resistance. Ninety-six doubled-haploid (DH)rice lines of an indica and japonica cross were grown in both flooding and upland conditions and QTLs for morphological traits at seedling stage were examined using 208 restriction fragment length polymorphism (RFLP) and 76 microsatellite (SSR) markers. A total of 32 putative QTLs were associated with the four seedling traits: average of three adventitious root lengths (ARL), shoot height (SH), shoot biomass (SW), and root to shoot dry weight ratio (RSR). Five QTLs detected were the same under control and upland conditions. The ratio between the mean value of the seedling trait under upland and flooding conditions was used for assessing drought tolerance. A total of six QTLs for drought tolerance were detected. Comparative analysis was performed for the QTLs detected in this case and those reported from two other populations with the same upland rice variety Azucena as parent. Several identical QTLs for seedling elongation across the three populations with the positive alleles from the upland rice Azucena were detected, which suggests that the alleles of Azucena might be involved in water stress-accelerated elongation of rice under different genetic backgrounds. Five cell wall-related candidate genes for OsEXP1, OsEXP2, OsEXP4, EXT, and EGase were mapped on the intervals carrying the QTLs for seedling traits.