Quantitative trait loci analysis for the developmental behavior of tiller number in rice (Oryza sativa L.)

 A doubled-haploid rice population of 123 lines from Azucena/IR64 was used for analyzing the developmental behavior of tiller number by conditional and unconditional QTL mapping methods. It was indicated that the number of QTLs significantly affecting tiller number was different at different measuring stages. Many QTLs controlling tiller growth identified at the early stages were undetectable at the final stage. Only one QTL could be detected across the whole growth period. By conditional QTL mapping, more QTLs for tiller number could be detected than that by unconditional mapping. The temporal patterns of gene expression for tiller number could be different at different stages. Even an individual gene or genes at the same genomic region might have opposite genetic effects at various growth stages. Received: 7 July 1997 / Accepted: 10 February 1998     

Mapping of the QTL (quantitative trait locus) conferring partial resistance to leaf blast in rice cultivar Chubu 32

The rice cultivar Chubu 32 possesses a high level of partial resistance to leaf blast. The number and chromosomal location of genes conferring this resistance were detected by restriction fragment length polymorphism (RFLP) linkage mapping and quantitative trait locus (QTL) analysis. For the mapping, 149 F₃ lines derived from the cross between rice cultivar Norin 29, with a low level of partial resistance, and Chubu 32 were used, and their partial resistance to leaf blast was assessed in upland nurseries. A linkage map covering six chromosomes and consisting of 36 RFLP markers was constructed. In the map, only one significant QTL (LOD>2.0) for partial resistance was detected on chromosome 11. This QTL explained 45.6% of the phenotypic variation. The segregation ratio of the F3 lines was 3:1 for partial resistance to susceptibility. These results suggest that the partial resistance in Chubu 32 is controlled by a major gene. Received: 15 March 2001 / Accepted: 13 August 2001     

Analyzing quantitative trait loci for yield using a vegetatively replicated F2 population from a cross between the parents of an elite rice hybrid

Although F₂s are the most informative populations for genetic analysis, it has been difficult to use F₂ populations directly for QTL analysis because it is usually difficult to assess the reliability of the data, due to an inability to estimate the experimental errors. In this study, we performed a QTL analysis for yield and yield-component traits of an F₂ population based on data from replicated field trials over 2 years using vegetative shoots of ratooned plants, making use of the ratooning habit of rice. The objective of this study was to explore the possibility of conducting QTL analyses directly based on an F₂ population by means of ratooning plants. The experimental population was from a cross between ’Zhenshan 97’ and ’Minghui 63’, the parents of ’Shanyou 63’, an elite rice hybrid widely grown in China. A genetic linkage map containing 151 molecular markers was constructed for QTL mapping. A total of 20 distinct QTLs were detected; eight of these were detected in both years and remaining 12 in only 1 year. Compared with the results of our previous analysis of the F_2:3 families from the same cross, it was shown that most of the QTLs detected in the ratooned F₂ population were also detected in the F_2:3 population. However, the estimates of both additive and dominant types of genetic effects for many of the QTLs based on F₂ ratoons were substantially larger than those based on F_2:3 families. The results indicate that vegetatively ratooned F₂ populations may have considerable utility in the mapping of QTLs, especially if dominant types of gene actions are of concern, although there were certain technical limitations in making use of such populations in the experiments. Received: 11 November 1999 / Accepted: 24 November 1999     

Mapping quantitative trait loci for milling quality, protein content and color characteristics of rice using a recombinant inbred line population derived from an elite rice hybrid

Milling properties, protein content, and flour color are important factors in rice. A marker-based genetic analysis of these traits was carried out in this study using recombinant inbred lines (RILs) derived from an elite hybrid cross ’Shanyou 63’, the most-widely grown rice hybrid in production in China. Correlation analysis shows that the traits were inter-correlated, though the coefficients were generally small. Quantitative trait locus (QTL) analysis with both interval mapping (IM) and composite interval mapping (CIM) revealed that the milling properties were controlled by the same few loci that are responsible for grain shape. The QTL located in the interval of RM42-C734b was the major locus for brown rice yield, and the QTL located in the interval of C1087-RZ403 was the major locus for head rice yield. These two QTLs are the loci for grain width and length, respectively. The Wx gene plays a major role in determining protein content and flour color, and is modified by several QTLs with minor effect. The implications of the results in rice breeding were discussed. Received: 15 September 2000 / Accepted: 31 March 2001     

Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags

We have constructed a rice function map by collating the results on quantitative trait loci (QTLs) for 23 important physiological and agronomic characters (including 13 newly measured traits) obtained using backcross inbred lines of japonica Nipponbare×indica Kasalath. Using these materials, The Rice Genome project (RGP) has developed a high-density genetic map. QTLs controlling yield did not overlap with those controlling the morphological and physiological traits supposed to relate to yield, such as photosynthetic ability. This result suggests that these traits do not influence yield, at least in this genetic background and environment. QTLs controlling yield also did not overlap with the structural genes controlling carbon metabolism (rbcS, cytosolic or plastidic fructose-1,6-bisphosphate, R-enzyme, and sucrose synthase).The combination of a function map and results from the RGP can be advantageous. The utility of this map is discussed. Received: 1 October 1999 / Accepted: 28 July 2000     

Identification of quantitative trait loci and epistatic interactions for plant height and heading date in rice

Appropriate heading date and plant height are prerequisites for attaining the desired yield level in rice breeding programs. In this study, we analyzed the genetic bases of heading date and plant height at both single- locus and two-locus levels, using a population of 240 F_2:3 families derived from a cross between two elite rice lines. Measurements for the traits were obtained over 2 years in replicated field trials. A linkage map was constructed with 151 polymorphic marker loci, based on which interval mapping was performed using Mapmaker/QTL. The analyses detected six QTLs for plant height and six QTLs for heading date; collectively the QTLs for heading date accounted for a much greater amount of phenotypic variation than did the QTLs for plant height. Two-way analyses of variance, with all possible two-locus combinations, detected large numbers (from 101 to 257) of significant digenic interactions in the 2 years for both traits involving markers distributed in the entire genome; 22 and 39 were simultaneously detected in both years for plant height and heading date, respectively. Each of the interactions individually accounted for only a very small portion of the phenotypic variation. The majority of the significant interactions involved marker loci that did not detect significant effects by single-locus analyses, and many of the QTLs detected by single-locus analyses were involved in epistatic interactions. The results clearly demonstrated the importance of epistatic interactions in the genetic bases of heading date and plant height. Received: 5 May 2001 / Accepted: 3 August 2001     

Mapping QTLs for phosphorus deficiency tolerance in rice (Oryza sativa L.)

 The amplified fragment length polymorphism (AFLP) technique combined with selective genotyping was used to map quantitative trait loci (QTLs) associated with tolerance for phosphorus (P) deficiency in rice. P deficiency tolerant cultivar IR20 was crossed to IR55178-3B-9-3 (sensitive to P-deficiency) and 285 recombinant inbred lines (RILs) were produced by single-seed descent. The RILs were phenotyped for the trait by growing them in P-sufficient (10.0 mg/l) and P-deficient (0.5 mg/l) nutrient solution and determining their relative tillering ability at 28 days after seeding, and relative shoot dry weight and relative root dry weight at 42 days after seeding. Forty two of each of the extreme RILs (sensitive and tolerant) and the parents were subjected to AFLP analysis. A map consisting of 217 AFLP markers was constructed. Its length was 1371.8 cM with an average interval size of 7.62 cM. To assign linkage groups to chromosomes, 30 AFLP and 26 RFLP markers distributed over the 12 chromosomes were employed as anchor markers. Based on the constructed map, a major QTL for P-deficiency tolerance, designated PHO, was located on chromosome 12 and confirmed by RFLP markers RG9 and RG241 on the same chromosome. Several minor QTLs were mapped on chromosomes 1, 6, and 9. Received: 21 April 1998 / Accepted: 9 June 1998     

Power analysis for quantitative trait locus mapping in populations derived by multiple backcrosses

 Populations derived by multiple backcrosses are potentially useful for quantitative trait locus (QTL) mapping studies. Comparisons of relative power to detect QTL using populations derived by multiple back-crosses are needed to make decisions when mapping projects are initiated. The objective of this study was to theoretically compare the power to detect QTL in populations derived by multiple backcrosses relative to mapping in a recombinant inbred population of equal size. Backcrossing results in a reduction in genetic variance with each generation and also results in an increasing frequency of the recurrent parent marker genotype. The relevant outcome for QTL mapping is a reduction in genetic variance to partition between marker genotype classes and increasing unbalance of the number of individuals contributing to the mean of the marker genotypes. Both of these factors lead to a decrease in the power to detect a QTL as the number of backcross generations increases. Experimental error was held constant with the populations compared. From a theoretical standpoint, backcross-derived populations offer few advantages for QTL detection. If, however, a backcrossing approach is the most efficient method to achieve a desired breeding objective and if QTL detection is an objective of equal or less importance, backcross-derived populations are a reasonable approach to QTL detection. Received: 4 August 1996 / Accepted: 4 April 1997     

水稻种子贮藏10年后的活力相关基因定位

以2004年构建并保存在种质库10年的186个单株组成的湘743/Katy F2:3群体为材料,在发芽的第5天和第9天统计亲本和各株系的发芽率和成苗率,应用由129个标记组成的连锁图谱检测与种子活力相关的QTL,一共检测到12个QTLs,共分布在6条染色体的6个区间,单个QTLs对群体性状表型变异的贡献率为5.73%~47.53%,联合贡献率都是50%。其中,在第8染色体RM152~RM310区间检测到一个主效的QTL,对第5天发芽率和第9天发芽率和第9天成苗率的贡献率分别为12.02%、47.53%、38.64%,来自于湘743的基因增加发芽率和成苗率;在第9染色体RM444~RM219区间检测到一个稳定表达的QTL,对第5天发芽率和第9天发芽率和第9天成苗率的贡献率分别为8.85%、7.49%、10.36%,来自于Katy的基因增加发芽率和成苗率;此外,没有检测到显著的上位性互作。     

Genetic bases of instability of male sterility and fertility reversibility in photoperiod-sensitive genic male-sterile rice

Photoperiod-sensitive genetic male-sterile (PSGMS) rice, with its male fertility regulated by photoperiod length, is very useful for hybrid rice development. However, breeding for new PSGMS lines has faced two major difficulties – the stability of male sterility and the reversibility of male fertility. In this study we assessed the genetic bases of stability of sterility and fertility reversibility using a molecular marker-based approach. A cross was made between two newly bred PSGMS lines: Peiai 64S, which has a stable sterility but is difficult to reverse to fertility, and 8902S, which has a unstable sterility but is easy to reverse to fertility. The fertility of the parents and of the F₁ and F₂ populations was repeatedly examined under 11 different long-day and short-day conditions. The genetic effects were assayed by interval mapping and two-way analyses of variance using the F₂ data of 128 polymorphic loci representing all the 12 rice chromosomes. The analyses resolved a number of single-locus QTLs and two-locus interactions under both long-day and short day conditions. The interactions involved a large number of loci, most of which were not detectable on a single-locus basis. The results showed that the genetic bases of both stability of sterility and reversibility of fertility are the joint effects of the additive effects of the QTLs and additive-by-additive components of two-locus interactions. The implications of these findings in hybrid rice development are also discussed. Received: 11 January 1999 / Accepted: 19 January 1999     

Genome‐wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure

The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co‐localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked‐down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.     

Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors

 Fine mapping was carried out on three putative QTLs (tentatively designated as Hd-1 to Hd-3) of five such QTLs controlling heading date in rice that had been earlier identified using an F₂ population derived from a cross between a japonica variety, ‘Nipponbare’, and an indica variety, ‘Kasalath’, using progeny backcrossed with ‘Nipponbare’ as the recurrent parent. One BC₃F₂ and two BC₃F₁ plants, in which the target QTL regions were heterozygous and most other chromosomal regions were homozygous for the ‘Nipponbare’ allele, were selected as the experimental material. Self-pollinated progeny (BC₃F₂ and BC₃F₃) of the BC₃F₁ or BC₃F₂ showed continuous variation in days to heading. By means of progeny testing based on BC₃F₃ or BC₃F₄ lines, we determined the genotypes of each BC₃F₂ or BC₃F₃ individual at target QTLs. Their segregation patterns fitted Mendelian inheritance ratios. When the results obtained by RFLP analysis and progeny tests were combined, Hd-1, Hd-2 and Hd-3 were mapped precisely on chromosomes 6, 7 and 6, respectively, of a rice RFLP linkage map. The results demonstrated that QTLs can be treated as Mendelian factors. Moreover, these precise locations were in good agreement with the regions estimated by QTL analysis of the initial F₂ population, demonstrating the high reliability of QTL mapping using a high-density linkage map. Received: 5 November 1997 / Accepted: 10 February 1998     

Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice

Rice is often found as various weedy forms in temperate or newly cultivated rice growing regions throughout the world. The emergence of these forms in the absence of true wild rice remains unclear. A genetic analysis of domestication-related traits (weed syndrome) has been conducted to better understand the appearance of these plants in rice fields. A doubled haploid (DH) population was derived from a cross between a japonica variety and a weedy plant collected in Camargue (France) to set up a genetic linkage map consisting of 68 SSR and 31 AFLP loci. Five qualitative traits related to pigmentation of different organs and 15 developmental and morphological quantitative traits were scored for genes and QTLs mapping. Despite a good reactivity in anther culture and a high fertility of the DH lines, segregation distortions were observed on chromosomal segments bearing gametophytic and sterility genes and corresponded to various QTLs evidenced in indica×japonica distant crosses. Mapping of the coloration genes was found to be in agreement with the presence of several genes previously identified and according to the genetic model governing the synthesis and distribution of anthocyan pigment in the plant. In addition, the main specific traits of weedy forms revealed the same genes/QTLs as progeny derived from a cross between Oryza sativa and its wild progenitor O. rufipogon. A large variation for most characters was found in the DH population, including transgressive variation. Significant correlations were observed between morphology and traits related to weeds and corresponded to a distinct colocalization of most of the QTLs on a limited number of chromosomal regions. The significance of these results on the origin of weedy forms and the de-domestication process is discussed. Received: 25 February 2000 / Accepted: 14 April 2000     

Quantitative trait loci for grain quality, productivity, morphological and agronomical traits in sorghum (Sorghum bicolor L. Moench)

 Quantitative trait loci (QTLs) for grain quality, yield components and other traits were investigated in two Sorghum caudatum×guinea recombinant inbred line (RIL) populations. A total of 16 traits were evaluated (plant height, panicle length, panicle compactness, number of kernels/panicle, thousand-kernel weight, kernel weight/panicle, threshing percentage, dehulling yield, kernel flouriness, kernel friability, kernel hardness, amylose content, protein content, lipid content, germination rate and molds during germination and after harvest) and related to two 113- and 100-point base genetic maps using simple (SIM) and composite (CIM) interval mapping. The number, effects and relative position of QTLs detected in both populations were generally in agreement with the distributions, heritabilities and correlations among traits. Several chromosomal segments markedly affected multiple traits and were suspected of harbouring major genes. The positions of these QTLs are discussed in relation to previously reported studies on sorghum and other grasses. Many QTLs, depending on their relative effects and position, could be used as targets for marker-assisted selection and provide an opportunity for accelerating breeding programmes. Received: 14 February 1998 / Accepted: 4 March 1998     

QTL mapping for the paste viscosity characteristics in rice (Oryza sativa L.)

In order to understand the genetic basis of the paste viscosity characteristics (RVA profile, which is tested on the Rapid Visco Analyser) of the rice grain, we mapped QTLs for RVA profile parameters using a DH population derived from a cross between an indica variety, Zai-Ye-Qing 8 (ZYQ8), and a japonica variety, Jing-Xi 17 (JX17). Evidence of genotype-by-environment interaction was found by comparing the mapped QTLs between two locations, Hainan (HN) and Hangzhou (HZ). A total of 20 QTLs for six parameters of the RVA profiles were identified at least one location. Only the waxy locus (wx) located on chromosome 6 was detected significantly at both environments for five traits, i.e. hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BDV), consistency viscosity (CSV) and setback viscosity (SBV). This locus explained 19.5%–63.7% of the total variations at both environments, suggesting that the RVA profiles were mainly controlled by the wx gene. HPV, CPV, BDV, CSV and SBV were also controlled by other QTLs whose effects on the respective parameter were detected only in one environment, while for the peak viscosity (PKV), only 2 QTLs, 1 at HN,the other at HZ, were identified. These results indicate that RVA profiles are obviously affected by environment. Received: 18 July 1999 / Accepted: 27 August 1999     

Mapping quantitative trait loci for seedling vigor in rice using RFLPs

Improving seedling vigor is an important objective of modern rice (Oryza saliva L.) breeding programs. The purpose of this study was to identify and map quantitative trait loci (QTL) underlying seedling vigor-related traits using restriction fragment length polymorphisms (RFLPs). An F₂ population of 204 plants was developed from a cross between a low-vigor japonica cultivar Labelle (LBL) and a high-vigor indica cultivar Black Gora (BG). A linkage map was constructed of 117 markers spanning 1496 Haldane cM and encompassing the 12 rice chromosomes with an average marker spacing of 14 cM. The length of the shoots, roots, coleoptile and mesocotyl were measured on F₃ families in slantboard tests conducted at two temperatures (18° and 25°C). By means of interval analysis, 13 QTLs, each accounting for 7% to 38% of the phenotypic variance, were identified and mapped in the two temperature regimes at a log-likelihood (LOD) threshold of 2.5. Four QTLs controlled shoot length, 2 each controlled root and coleoptile lengths and 5 influenced mesocotyl length. Single-point analysis confirmed the presence of these QTLs and detected additional loci for shoot, root and coleoptile lengths, these latter usually accounting for less than 5% of the phenotypic variation. Only 3 QTLs detected both by interval and singlepoint analyses were expressed under both temperature regimes. Additive, dominant and overdominant modes of gene action were observed. Contrary to what was predicted from parental phenotype, the low-vigor LBL contributed 46% of the positive alleles for shoot, root and coleoptile lengths. Positive alleles from the high-vigor parent BG were identified for increased root, coleoptile and mesocotyl lengths. However, BG contributed alleles with only minor effects for shoot length, the most important determinant of seedling vigor in water-seeded rice, suggesting that it would not be an ideal donor parent for introducing faster shoot growth alleles into temperate japonica cultivars.     

Estimation of the contribution of quantitative trait loci (QTL) to the variance of a quantitative trait by means of genetic markers

The estimation of the contribution of an individual quantitative trait locus (QTL) to the variance of a quantitative trait is considered in the framework of an analysis of variance (ANOVA). ANOVA mean squares expectations which are appropriate to the specific case of QTL mapping experiments are derived. These expectations allow the specificities associated with the limited number of genotypes at a given locus to be taken into account. Discrepancies with classical expectations are particularly important for two-class experiments (backcross, recombinant inbred lines, doubled haploid populations) and F₂ populations. The result allows us firstly to reconsider the power of experiments (i.e. the probability of detecting a QTL with a given contribution to the variance of the trait). It illustrates that the use of classical formulae for mean squares expectations leads to a strong underestimation of the power of the experiments. Secondly, from the observed mean squares it is possible to estimate directly the variance associated with a locus and the fraction of the total variance associated to this locus (r _l ² ). When compared to other methods, the values estimated using this method are unbiased. Considering unbiased estimators increases in importance when (1) the experimental size is limited; (2) the number of genotypes at the locus of interest is large; and (3) the fraction of the variation associated with this locus is small. Finally, specific mean squares expectations allows us to propose a simple analytical method by which to estimate the confidence interval of r _l ² . This point is particularly important since results indicate that 95% confidence intervals for r _l ² can be rather wide:2–23% for a 10% estimate and 8–34% for a 20% estimate if 100 individuals are considered.     

Identification of quantitative trait loci influencing annual height- and diameter-increment growth in loblolly pine (Pinus taeda L.)

 Quantitative trait loci (QTLs) for annual height- and diameter-increment growth were estimated in each of two three-generation loblolly pine pedigrees. Annual height-increment was measured in three consecutive years in the BASE pedigree and in four consecutive years in the QTL pedigree. Annual diameter-increment was measured only in the QTL pedigree for two consecutive years. An interval mapping-approach was used to estimate the number of QTLs, the magnitude of QTL effects, and their position on genetic linkage maps. Thirteen different height-increment and eight different diameter-increment QTLs were detected, suggesting that the these traits are, at least in part, controlled by a few genes of large effect. Little evidence was found for the expression of individual QTLs in multiple years or in multiple genetic backgrounds. These results were discussed in terms of the power of the experiment and their consequences for marker-assisted breeding. Received: 12 July 1998/Accepted: 5 August 1998     

A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway

Grain size is one of the essential components determining rice yield and is a target for both domestication and artificial breeding. Gibberellins (GAs) are diterpenoid phytohormones that influence diverse aspects of plant growth and development. Several quantitative trait loci (QTLs) have been identified that control grain size through phytohormone regulation. However, little is known about the role of GAs in the control of grain size. Here we report the cloning and characterization of a QTL, GW6 (GRAIN WIDTH 6), which encodes a GA‐regulated GAST family protein and positively regulates grain width and weight. GW6 is highly expressed in the young panicle and increases grain width by promoting cell expansion in the spikelet hull. Knockout of GW6 exhibits reduced grain size and weight, whereas overexpression of GW6 results in increased grain size and weight. GW6 is induced by GA and its knockout downregulates the expression of GA biosynthesis genes and decreases GA content in the young panicle. We found that a natural variation in the cis element CAAT‐box in the promoter of GW6 is associated with its expression level and grain width and weight. Furthermore, introduction of GW6 to Oryza indica variety HJX74 can lead to a 10.44% increase in rice grain yield, indicating that GW6 has great potential to improve grain yield in rice.     

QTLs influencing panicle size detected in two reciprocal introgressive line (IL) populations in rice (Oryza sativa L.)

Two sets of reciprocal introgression line (IL) populations, i.e., ILs with Lemont as recurrent parent (IL_LT) and ILs with Teqing as recurrent parent (IL_TQ), were developed and evaluated for traits representing panicle size, including primary branch number (PBN), secondary branch number (SBN), and spikelet number per panicle (SNP). Together with the regression to recurrent parent by advanced backcross, transgressive segregations were observed for all traits. Correlation and regression analysis showed that SBN had much higher contribution to SNP than PBN. It was confirmed by the QTL analysis that many common loci were detected between SBN and SNP, in comparison with single common locus between PBN and SNP. One and three main effect QTLs (M-QTLs) were detected for PBN in IL_LT and IL_TQ, respectively. Six M-QTLs per trait per populations were associated with SBN and SNP. Less number and lower contribution of epistasis were detected in IL populations in comparison with mapping result from F ₂ or RI population. There were only four QTLs in fourteen loci (near 30%) commonly detected in both reciprocal IL populations implying the large impact of genetic background on QTLs expression. H. W. Mei and J. L. Xu contributed equally to this work.