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 aluminum tolerance in rice (Oryza sativa L.) at different seedling stages

To investigate the genetic background for aluminum (Al) tolerance in rice, a recombinant inbred (RI) population, derived from a cross between an Al-sensitive lowland indica rice variety IR1552 and an Al-tolerant upland japonica rice variety Azucena, was used in culture solution. A molecular linkage map, together with 104 amplified fragment length polymorphism (AFLP) markers and 103 restriction fragment length polymorphism (RFLP) markers, was constructed to map quantitative trait loci (QTLs) and epistatic loci for Al tolerance based on the segregation for relative root length (RRL) in the population. RRL was measured after stress for 2 and 4 weeks at a concentration of 1mM of Al³⁺ and a control with a pH 4.0, respectively. Two QTLs were detected at both the 2nd and the 4th weeks on chromosomes 1 and 12 from unconditional mapping, while the QTL on chromosome 1 was only detected at the 2nd stress week from conditional mapping. The effect of the QTL on chromosome 12 was increased with an increase of the stress period from 2 to 4 weeks. The QTL on chromosome 1 was expressed only at the earlier stress, but its contribution to tolerance was prolonged during growth. At least one different QTL was detected at the different stress periods. Mean comparisons between marker genotypic classes indicated that the positive alleles at the QTLs were from the Al-tolerant upland rice Azucena. An important heterozygous non-allelic interaction on Al tolerance was found. The results indicated that tolerance in the younger seedlings was predominantly controlled by an additive effect, while an epistatic effect was more important to the tolerance in older seedlings; additionally the detected QTLs may be multiple allelic loci for Al tolerance and phosphorus-uptake efficiency, or for Al and Fe²⁺ tolerance. Received: 29 July 1999 / Accepted: 13 October 1999     

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.     

Quantitative trait loci controlling resistance to cadmium rhizotoxicity in two recombinant inbred populations of Arabidopsis thaliana are partially shared by those for hydrogen peroxide resistance

To understand mechanisms of cadmium (Cd) tolerance variation associated with root elongation in Arabidopsis thaliana , quantitative trait loci (QTLs) and epistasis were analyzed using relative root length (RRL: % of the root length in +Cd to −Cd) as a tolerant index. Using the composite interval mapping method, three major QTLs ( P < 0.05) were detected on chromosomes 2, 4 and 5 in the recombinant inbred population derived from a cross between Landsberg erecta (L er −0) and Columbia (Col-4). The highest logarithm of odds (LOD) of 5.6 was detected with the QTL on chromosome 5 (QTL5), which is linked to the genetic marker CDPK9 and explained about 26% of the Cd tolerance variation. There was no significant difference in Cd-translocation ratio from roots to shoots between tolerant and sensitive recombinant inbreed lines (RILs), while greater accumulations of reactive oxygen species were observed in the roots of sensitive RILs. This suggested that accumulation of ROS would explain Cd tolerance variation of the L er /Col RILs, which is mainly controlled by the QTL on chromosome 5. The QTL5 in L er /Col population was also detected as one of the major QTLs controlling tolerances to hydrogen peroxide and to copper, which is another ROS generating rhizotoxic metal. The same chromosomal position was detected as a common major QTL for Cd and hydrogen peroxide tolerances in a different recombinant inbreed (RI) population derived from a cross of Col- gl1 and Kashmir (Kas-1). These data, along with a multitraits QTL analysis in both sets of RILs, suggest that peroxide damage depends on the genotype at a major Cd-tolerant locus on the upper part of chromosome 5.     

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     

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     

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     

Mapping QTLs for root traits under different nitrate levels at the seedling stage in maize (Zea mays L.)

Nitrogen (N) loss is a worldwide problem in crop production. Apart from reasonable N fertilizer application, breeding N efficient cultivars provides an alternative way. Root architecture is an important factor determining N acquisition. However, little is known about the molecular genetic basis for root growth in relation to N supply. In the present study, an F₈ maize (Zea may L.) recombinant inbred (RI) population consisting of 94 lines was used to identify the QTLs for root traits under different nitrate levels. The lateral root length (LRL), axial root length (ARL), maximal axial root length (MARL), axial root number (ARN) and average axial root length (AARL) were evaluated under low N (LN) and high N (HN) conditions in a hydroponics system. A total of 17 QTLs were detected among which 14 loci are located on the same chromosome region as published QTLs for root traits. A major QTL on chromosome 1 (between bnlg1025 and umc2029) for the AARL under LN could explain 43.7% of the phenotypic variation. This QTL co-localizes with previously reported QTLs that associate with root traits, grain yield, and N uptake. Our results indicate that longer axial roots are important for efficient N acquisition and the major QTL for AARL may be used as a marker in breeding N efficient maize genotypes.     

Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations

To understand the types of gene action controlling seven quantitative traits in rice, we carried out quantitative trait locus (QTL) mapping in order to distinguish between the main-effect QTLs (M-QTLs) and digenic epistatic QTLs (E-QTLs) responsible for the trait performance of 254 recombinant inbred lines (RILs) from rice varieties Lemont/Teqing and two backcross hybrid (BCF₁) populations derived from these RILs. We identified 44 M-QTL and 95 E-QTL pairs in the RI and BCF₁ populations as having significant effects on the mean values and mid-parental heterosis of heading date, plant height, flag leaf length, flag leaf width, panicle length, spikelet number and spikelet fertility. The E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both the RI and BCF₁ populations. In both BCF₁ populations, over-dominant (or under-dominant) loci were more important than additive and complete or partially dominant loci for M-QTLs and E-QTL pairs, thereby supporting prior findings that overdominance resulting from epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice.     

Natural variation of <Emphasis Type="Italic">Arabidopsis thaliana </Emphasis>reveals that aluminum resistance and proton resistance are controlled by different genetic factors

Root growth of Arabidopsis thaliana is inhibited by proton rhizotoxicity in low ionic strength media when the pH of the medium is lower than 5.0. QTL analysis at pH 4.7 revealed that two major QTLs on chromosome 2 and 5 and an additional six epistatic interacting loci pairs control proton resistance in the Ler/Col recombinant inbred population. These genetic factors are independently associated with proton resistance in comparison to the known Al resistant QTL and epistases detected in the same RI population at 4 μM Al at pH 5.0. This indicates that different genetic factors regulate mechanisms of resistance to each stress in this plant species. No correlation was observed between proton resistance and Al resistance among 260 accessions indicating that there is no simple relationship between the genetic factors controlling each trait. Several accessions with different combinations of proton (pH 4.7) and Al (4 μM Al at pH 5.0) resistances were identified by phenotypic cluster analysis. Although this grouping was performed using root growth data, the degree of resistance was correlated with their sensitivity to short-term damage in the root tip, indicating that the same resistance mechanism controls proton resistance at different time scales. Resistant accessions grew better than sensitive ones in acid soil culture. This suggests that proton resistance in hydroponic conditions could be an important index in breeding programs to improve productivity in acid soil, at least in acid sensitive plant species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Quantitative trait loci for aluminum resistance in wheat

Quantitative trait loci (QTL) for wheat resistance to aluminum (Al) toxicity were analyzed using simple sequence repeats (SSRs) in a population of 192 F₆ recombinant inbred lines (RILs) derived from a cross between an Al-resistant cultivar, Atlas 66 and an Al-sensitive cultivar, Chisholm. Wheat reaction to Al was measured by relative root growth and root response to hematoxylin stain in nutrient-solution culture. After screening 1,028 SSR markers for polymorphisms between the parents and bulks, we identified two QTLs for Al resistance in Atlas 66. One major QTL was mapped on chromosome 4D that co-segregated with the Al-activated malate transporter gene (ALMT1). Another minor QTL was located on chromosome 3BL. Together, these two QTLs accounted for about 57% of the phenotypic variation in hematoxylin staining score and 50% of the variation in net root growth (NRG). Expression of the minor QTL on 3BL was suppressed by the major QTL on 4DL. The two QTLs for Al resistance in Atlas 66 were also verified in an additional RIL population derived from Atlas 66/Century. Several SSR markers closely linked to the QTLs were identified and have potential to be used for marker-assisted selection (MAS) to improve Al-resistance of wheat cultivars in breeding programs.     

Quantitative Trait Loci for Aluminum Resistance in Wheat Cultivar Chinese Spring

Aluminum (Al) toxicity is one of the major constrains for wheat production in many wheat growing areas worldwide. Further understanding of inheritance of Al resistance may facilitate improvement of Al resistance of wheat cultivars (Triticum aestivum L.). A set of ditelosomic lines derived from the moderately Al-resistant wheat cultivar Chinese Spring was assessed for Al resistance. The root growth of ditelosomic lines DT5AL, DT7AL, DT2DS and DT4DS was significantly lower than that of euploid Chinese Spring under Al stress, suggesting that Al-resistance genes might exist on the missing chromosome arms of 5AS, 7AS, 2DL and 4DL of Chinese Spring. A population of recombinant inbred lines (RILs) from the cross Annong 8455 × Chinese Spring-Sumai 3 7A substitution line was used to determine the effects of these chromosome arms on Al resistance. A genetic linkage map consisting of 381 amplified fragment length polymorphism (AFLP) markers and 168 simple sequence repeat (SSR) markers was constructed to determine the genetic effect of the quantitative trait loci (QTLs) for Al resistance in Chinese Spring. Three QTLs, Qalt.pser-4D, Qalt.pser-5A and Qalt.pser-2D, were identified that enhanced root growth under Al stress, suggesting that inheritance of Al resistance in Chinese Spring is polygenic. The QTL with the largest effect was flanked by the markers of Xcfd23 and Xwmc331 on chromosome 4DL and most probably is multi-allelic to the major QTL identified in Atlas 66. Two additional QTLs, Qalt.pser-5A and Qalt.pser-2D on chromosome 5AS and 2DL, respectively, were also detected with marginal significance in the population. Some SSR markers identified in this study would be useful for marker-assisted pyramiding of different QTLs for Al resistance in wheat cultivars.     

Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers

This research was undertaken to identify and map quantitative trait loci (QTLs) associated with five parameters of rice root morphology and to determine if these QTLs are located in the same chromosomal regions as QTLs associated with drought avoidance/tolerance. Root thickness, root:shoot ratio, root dry weight per tiller, deep root dry weight per tiller, and maximum root length were measured in three replicated experiments (runs) of 203 recombinant inbred lines grown in a greenhouse. The lines were from a cross between indica cultivar Co39 andjaponica cultivar Moroberekan. The 203 RI lines were also grown in three replicated field experiments where they were drought-stressed at the seedling, early vegetative, and late-vegetative growth stage and assigned a visual rating based on leaf rolling as to their degree of drought avoidance/tolerance. The QTL analysis of greenhouse and field data was done using single-marker analysis (ANOVA) and interval analysis (Mapmaker QTL). Most QTLs that were identified were associated with root thickness, root/shoot ratio, and root dry weight per tiller, and only a few with deep root weight. None were reliably associated with maximum root depth due to genotype-by-experiment interaction. Root thickness and root dry weight per tiller were the characters found to be the least influenced by environmental differences between greenhouse runs. Correlations of root parameters measured in greenhouse experiments with field drought avoidance/tolerance were significant but not highly predictive. Twelve of the fourteen chromosomal regions containing putative QTLs associated with field drought avoidance/tolerance also contained QTLs associated with root morphology. Thus, selecting for Moroberekan alleles at marker loci associated with the putative root QTLs identified in this study may be an effective strategy for altering the root phenotype of rice towards that commonly associated with drought-resistant cultivars.     

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     

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.     

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.     

The genetic control of tolerance to aluminum toxicity in the ‘Essex’ by ‘Forrest’ recombinant inbred line population

Aluminum (Al) toxicity to plant roots is a major problem of acidic soils. The main chemical reaction involved is Al hydrolysis. Application of lime or nitrate fertilizers to raise soil pH reduces Al toxicity but not as economically as a plant genotypes with natural tolerance against this stress. Ammonium fertilization of crops and assimilation of ammonium (even that derived from dinitrogen) are particularly acidifying of the root zone. The aims of the present study were to find genotypes of soybean tolerant to aluminum stress and identify QTL underlying that trait. Used were recombinant inbred lines (RILs) derived from the cross of ‘Essex’ by ‘Forrest’. RILs were grown in a greenhouse for 3 weeks and then transferred to hydroponics in a growth chamber. Root lengths (RL) were measured before and 72 h after Al treatment. RL before and after Al treatment were measured and used to calculate root tolerance index (RTI) and relative mean growth (RMG). RILs 1, 85, 40 and 83 had significant (P < 0.005) tolerance to Al stress judged by RL after Al, RTI and RMG. Eleven minor but significant marker–trait associations (P < 0.05) were detected using one-way ANOVA but only two major loci were significant in composite interval maps (LOD >3.0). The QTL on linkage group F (chromosome 13) was in the interval Satt160–Satt252 with a peak at 24 cM (peak LOD was 3.3). The QTL underlay 31% of trait variation and the Essex allele provided an additional 1.61 cm of root growth over 72 h in the presence of Al. The QTL on linkage group C2 (probably chromosome 4) was in the interval from Satt202 to Satt371 with a peak at 3.2 cM (peak LOD was 14.7). The QTL underlay 34% of trait variation or 1.81 cm of growth over 72 h in the presence of Al. Both loci encompassed genes implicated in citrate metabolism, a method of aluminum detoxification known to vary among soybean cultivars. Two major loci and at least nine minor loci were inferred to underlie tolerance to Al. RILs and markers may be used to select alleles that increase tolerance to soybean against Al stress.     

Fine Mapping QTL for Drought Resistance Traits in Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) Using Bulk Segregant Analysis

Drought stress is a major limitation to rice (Oryza sativa L.) yields and its stability, especially in rainfed conditions. Developing rice cultivars with inherent capacity to withstand drought stress would improve rainfed rice production. Mapping quantitative trait loci (QTLs) linked to drought resistance traits will help to develop rice cultivars suitable for water-limited environments through molecular marker-assisted selection (MAS) strategy. However, QTL mapping is usually carried out by genotyping large number of progenies, which is labour-intensive, time-consuming and cost-ineffective. Bulk segregant analysis (BSA) serves as an affordable strategy for mapping large effect QTLs by genotyping only the extreme phenotypes instead of the entire mapping population. We have previously mapped a QTL linked to leaf rolling and leaf drying in recombinant inbred (RI) lines derived from two locally adapted indica rice ecotypes viz., IR20/Nootripathu using BSA. Fine mapping the QTL will facilitate its application in MAS. BSA was done by bulking DNA of 10 drought-resistant and 12 drought-sensitive RI lines. Out of 343 rice microsatellites markers genotyped, RM8085 co-segregated among the RI lines constituting the respective bulks. RM8085 was mapped in the middle of the QTL region on chromosome 1 previously identified in these RI lines thus reducing the QTL interval from 7.9 to 3.8 cM. Further, the study showed that the region, RM212–RM302–RM8085–RM3825 on chromosome 1, harbours large effect QTLs for drought-resistance traits across several genetic backgrounds in rice. Thus, the QTL may be useful for drought resistance improvement in rice through MAS and map-based cloning.     

QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects

Grain length in rice plays an important role in determining rice appearance, milling, cooking and eating quality. In this study, the genetic basis of grain length was dissected into six main-effect quantitative trait loci (QTLs) and twelve pairs of epistatic QTLs. The stability of these QTLs was evaluated in four environments using an F₇ recombinant inbred line (RIL) population derived from the cross between a Japonica variety, Asominori, and an Indica variety, IR24. Moreover, chromosome segment substitution lines (CSSLs) harboring each of the six main-effect QTLs were used to evaluate gene action of QTLs across eight environments. A major QTL denoted as qGL-3a, was found to express stably not only in the isogenic background of Asominori but also in the recombinant background of Asominori and IR24 under multiple environments. The IR24 allele at qGL-3a has a positive effect on grain length. Based on the test of advanced backcross progenies, qGL-3a was dissected as a single Mendelian factor, i.e., long rice grain was controlled by a recessive gene gl-3. High-resolution genetic and physical maps were further constructed for fine mapping gl-3 by using 11 simple sequence repeat (SSR) markers designed using sequence information from seven BAC/PAC clones and a BC₄F₂ population consisting of 2,068 individuals. Consequently, the gl-3 gene was narrowed down to a candidate genomic region of 87.5 kb long defined by SSR markers RMw357 and RMw353 on chromosome 3, which provides a basis for map-based cloning of this gene and for marker-aided QTL pyramiding in rice quality breeding.     

Quantitative trait loci controlling root growth and architecture in Arabidopsis thaliana confirmed by heterogeneous inbred family

Arabidopsis thaliana provides a scientifically attractive and simple model for studying root growth and architecture and, subsequently, for discovering new genes involved in the control of these characters in plants. We have used the natural variation available in Arabidopsis accessions and mapped quantitative trait loci (QTLs) for primary root length (PRL), lateral root number (LRN) and density (LRD) and for total length of the lateral root system (LRL) in the Bay-0 × Shahdara population. Total phenotypic variation was very large, and despite the importance of the environmental component we were able to map 13 QTLs and one epistatic interaction between QTLs. Our results highlight the biological relevance and genetic control of lateral root density in this material. We were also able to show that variation in the extent of the lateral root system depends mainly on the growth of the existing lateral roots rather than in a change in LRN. Factors controlling lateral root growth seemed to have no major effect on primary root growth. Moreover, Shahdara QTL alleles always increased the length of the lateral roots, which may be taken as an adaptation to its very dry natural environment in Tadjikistan. A QTL for PRL was confirmed using a type of near-isogenic line called a heterogeneous inbred family (HIF), and this QTL is a candidate for further fine-mapping and cloning.