Mapping QTLs related to salinity tolerance of rice at the young seedling stage

Using a population of recombinant inbred lines of the 164 genotypes derived from a cross between ‘Milyang 23’ (indica) and ‘Gihobyeo’ (japonica) in rice (Oryza sativa L.), salt tolerance was evaluated at a young seedling stage in concentrations of 0.5% and 0.7% NaCl. Mapping quantitative trait loci (QTLs) related to salt tolerance was carried out by interval mapping using Qgene 3.0. Two QTLs (qST1 and qST3) conferring salt tolerance at young seedling stage were mapped on chromosome 1 and 3, respectively, and explained 35.5–36.9% of the total phenotypic variation in 0.5% and 0.7% NaCl. The favourable allele of qST1 was contributed by ‘Gihobyeo’, and that of qST3 by ‘Milyang 23’. The results obtained in 0.5% and 0.7% NaCl for 2 years were similar in flanked markers and phenotypic variation.     

Identification of salt tolerance‐improving quantitative trait loci alleles from a salt‐susceptible rice breeding line by introgression breeding

To improve salt tolerance of two elite rice varieties, Ce258 and Zhongguangxiang1 (ZGX1), two sets of introgression lines (ILs) each comprising 200 BC₁F₁₀ lines derived from a common donor, IR75862, and two recipient parents, Ce258 and ZGX1, were used for mapping of QTLs for four salt tolerance‐related traits at the seedling stage. Although the three parents were susceptible to salt, the two IL populations showed transgressive segregations for salt tolerance with 12 and 8 salt tolerance ILs in the Ce258‐ILs and ZGX1‐ILs. Eighteen main‐effect QTLs were identified for the four traits in the two IL populations, and the IR75862 alleles at most loci showed increased and decreased salt tolerance in the ZGX1 and Ce258 backgrounds, suggesting overwhelming genetic background effects on QTL detection for salt tolerance. The qDSS11 simultaneously detected in the two backgrounds was validated in a F₂ population derived from a salt tolerance line and ZGX1. Our results indicated that salt tolerance‐enhancing allele could be identified in the elite susceptible breeding lines and that introgression of the favourable alleles could facilitate the development of superior lines with greater salt tolerance levels.     

Quantitative trait loci mapping and stability for low temperature germination ability of rice

A high rate of germination at low temperatures is necessary for economic yields to be maintained. In this paper, the genetic control of low temperature germination ability (LTG) was assessed by the measurement of germination rate (GR), germination rate index (GI) and mean germination time (MGT), and genetically mapped using a set of recombinant inbred lines, derived from a cross between the japonica cultivar 'Asominori' and the indica cultivar 'IR24'. Putative quantitative trait loci (QTL) were validated by testing in two related sets of chromosome segment substitution lines (CSSL). In this genetic background, LTG is under the control of a number of QTL, each of relatively small effect, and is spread over six chromosomes. The most stable of these QTL was for GR, mapping to a segment of chromosome 11 which also carries a QTL for GI. On chromosome 2, qGR-2 not only controlled GR, but also was associated with GI and MGT. Significant differences in LTG were detected between 'Asominori' and some CSSL harbouring qGR-2 or qGR-11 .     

Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa×O. rufipogon BC1F7 population

Asian cultivated rice was domesticated from the wild rice, Oryza rufipogon and throughout the domestication process, a wide range of morphological and physiological changes altered the ancestral form. This study was conducted to identify the genetic basis of changes associated with the domestication process. An recombinant Inbred line (RIL) population consisting of 120 lines was developed from a cross between the Juponica cultivar.‘Hwayeongbyeo’and a presumed wild progenitor. O. rufipogon Griff. Acc.01944. The population was genotyped with 124 simple sequence length repeat (SSR) markers, providing an average interval size of 15 cM, and also evaluated for 20 traits related to domestication and agricultural performance. A total of 63 quantitative trait locus (QTLs) and one locus associated with qualitative variation for pericarp coloration were identified using single point and composite interval analysis. The number of QTLs per trait ranged from one to seven. Phenotypic variation associated with each QTL ranged from 3.7 to 40.4%. with an average of 15.3%. The results indicated that most domestication‐related traits clustered in chromosomal blocks, and the positions of many of these clusters were consistent with those reported in previous studies and with skewed segregation ratios in these BC₁,F₇ RILs. For 13 (20.6%) of the QTLs identified in this study. the O. rufipogan ‐derived allele contributed a desirable agronomic effect despite the overall undesirable characteristics of the wild phenotype. Favourable alleles from O. rufipogan were detected for panicle length, spikelets per panicle, days to heading and leaf discoloration associated with cold stress. When compared with previous studies involving interspecific crosses, it can be concluded that O. rufipogon is useful as a source of valuable alleles for rice improvement and that many of the introgressed regions contain genes that have a favourable impact on phenotype in different genetic backgrounds and different environments.     

Detecting major QTL associated with resistance to bacterial blight using a set of rice reciprocal introgression lines with high density SNP markers

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a worldwide rice disease. QTL providing BB resistance were identified using a set of introgression lines (ILs) derived from a cross between Teqing and Lemont, and 3924 evenly distributed SNP markers developed from the two parents. After inoculating three Xoo pathotypes, CII, CIV and CV, seven major BB resistance‐associated QTL were detected. The alleles at all loci with improved BB resistance were from the Teqing background. Four QTL resistance to CII and CIV were identified in the reciprocal backgrounds across 2 years. Six QTL conferring resistance to CV identified in Teqing background were not detected in Lemont background, indicating that genetic background had a strong effect on the BB resistance‐associated QTL. Based on the interactions of 27 significant digenic QTL pairs among the seven main‐effect QTL, the QTL were divided into three strain‐specific groups. Genotype analyses of resistant ILs suggest that rice lines with a high level of resistance to BB can be achieved by pyramiding R gene(s) and QTL that interact with R gene(s).     

Contribution of the grain size QTL GS3 to yield properties and physiological nitrogen-use efficiency in the large-grain rice cultivar ‘Akita 63’

The development of crop varieties with high nitrogen-use efficiency (NUE) is thought to be important in achieving sustainable cereal crop production. The high yield large-grain rice cultivar Oryza sativa L. ‘Akita 63’ (temperate japonica) has high physiological NUE (PNUE) for grain yield (GY). Our previous study revealed that a large-grain allele of GS3 is present in ‘Akita 63’. Here, we verified the influence of GS3 on the yield properties and PNUE for GY in ‘Akita 63’. The frequency distribution of brown rice length in F₂ crosses of ‘Iwate 75’ and ‘Akita 63’ showed a continuous distribution that could be explained by GS3. A near-isogenic line was developed to substitute the GS3 segment of ‘Koshihikari’, which harbours a normal-sized grain allele, in the genetic background of ‘Akita 63’ and the line was designated as Akita63NILGS3-Koshihikari. Compared with Akita63NILGS3-Koshihikari, ‘Akita 63’ exhibited a significantly increased grain length, single brown grain weight and GY, although no significant differences were observed in the nitrogen content and above-ground biomass per unit of cultivated area. These results indicate that the GS3 large-grain allele is a contributing factor to high PNUE for GY in ‘Akita 63’. These findings will facilitate the development of nitrogen-efficient rice varieties.     

Molecular mapping of a quantitative trait locus qSTV11Z harbouring rice stripe virus resistance gene,Stv‐b

Rice stripe virus (RSV) predominantly affects rice. In this study, we attempted to localize the quantitative trait locus (QTL) conferring RSV resistance in the ‘Zenith’ variety, which is known to harbour Stv‐a and Stv‐b. The resistant variety Zenith was crossed with the susceptible variety ‘Ilpum’ to generate a mapping population comprising 180 F_2:3 lines for QTL analysis. Contrary to previous findings, we could not detect Stv‐a‐specific QTLs on chromosome 6. Stv‐b‐specific QTL was detected on the long arm of chromosome 11; it was designated qSTV11^z. Six F_4:5 lines were selected from the F_3:4 population and fine‐mapped using insertion/deletion (InDel) markers. qSTV11^z was mapped to a 520‐kb region between the InDel markers Sid2 and Indel8. This region included OsSOT1 (candidate gene for STV11) and other previously reported RSV resistance QTLs. The OsSOT1 sequence in Ilpum and Zenith was identical to that of the susceptible variety ‘Koshihikari’, indicating that OsSOT1 is not the candidate gene of qSTV11^z. The localization of qSTV11^z should provide useful information for marker‐assisted selection and determination of genetic resources in rice breeding.     

Construction of chromosomal segment substitution lines and genetic dissection of introgressed segments associated with yield determination in the parents of a super‐hybrid rice

Heterosis is a phenomenon whereby hybrids of inbred lines produce favourable phenotypes that exceed those of their parents. Traits of interest are higher yield and stronger stress tolerance. The two‐line super‐hybrid rice ‘Liangyoupei9’ (LYP9) shows superiority to both its elite inbred line ‘93‐11’ and ‘Pei'ai64s’ (‘PA64s’) parents and conventional hybrids. However, the genetic basis of its hybrid vigour, especially yield determination, remains elusive. In the present study, a set of 156 chromosome segment substitution lines (CSSLs) carrying overlapping segments from ‘PA64s’ in a genetic background of ‘93‐11’ were constructed and planted in six environments. Three major agronomic traits, viz. panicle length (PL), heading date (HD) and plant height (PH), and five yield‐related traits, viz. grain weight per panicle (GWP), number of grains per panicle (GPP), 1000‐grain weight (TGW), seed set (SS) and number of panicles of per plant (PPP), were evaluated over 3 years. Quantitative trait loci (QTL) analysis was conducted using a likelihood ratio test based on stepwise regression. Forty‐six putative QTL distributed on 11 chromosomes were detected in more than one year. Remarkably, GWP of four CSSLs carrying positive yield QTL outperformed the recurrent parent ‘93‐11’ by more than 15%, in at least two environments. These results indicate that CSSLs are effective in identifying yield‐associated traits, and lines harbouring such QTL will be rich in resources for future molecular breeding programmes.     

Mapping of Quantitative Trait Loci Associated with Reproductive‐Stage Salt Tolerance in Rice

Salinity tolerance in rice varies with the state of growth, with the seedling and reproductive stages being the most sensitive. However, association between tolerances at the two stages is poor, suggesting that they are regulated by different processes and genes. Tolerance at the reproductive stage is the most crucial as it determines grain yield. An F₂ mapping population was developed from two rice genotypes contrasting in tolerance: Cheriviruppu and Pusa Basmati 1 (PB1). Cheriviruppu is highly tolerant at the reproductive stage, while PB1 is highly sensitive at both seedling and reproductive stages. One hundred and thirty‐one microsatellite markers polymorphic between the parents were used to construct a linkage map of 1458.5 cM (Kosambi), with a mean intermarker distance of 11.1 cM. Sixteen QTLs with LOD values ranging from 3.2 to 22.3 were identified on chromosomes 1, 7, 8 and 10, explaining 4–47 % of the phenotypic variation. The maximum number of QTL clusters for different component traits was colocalized on the long arm of chromosome 1 and chromosome 7. We identified several significant epistatic interactions, including three inter‐QTL interactions, using MapManager. The results suggest that pollen fertility, Na⁺ concentration and Na/K ratio in the flag leaf are the most important mechanisms controlling salt tolerance at the reproductive stage in rice. The study reports the construction of a genetic map for reproductive‐stage salt tolerance in rice and demonstrates its utility for molecular mapping of QTLs controlling salinity tolerance‐related traits, which will be useful in marker‐assisted selection in the future.     

Crop breeding for salt tolerance in the era of molecular markers and marker‐assisted selection

Crop salt tolerance (ST) is a complex trait affected by numerous genetic and non‐genetic factors, and its improvement via conventional breeding has been slow. Recent advancements in biotechnology have led to the development of more efficient selection tools to substitute phenotype‐based selection systems. Molecular markers associated with genes or quantitative trait loci (QTLs) affecting important traits are identified, which could be used as indirect selection criteria to improve breeding efficiency via marker‐assisted selection (MAS). While the use of MAS for manipulating simple traits has been streamlined in many plant breeding programmes, MAS for improving complex traits seems to be at infancy stage. Numerous QTLs have been reported for ST in different crop species; however, few commercial cultivars or breeding lines with improved ST have been developed via MAS. We review genes and QTLs identified with positive effects on ST in different plant species and discuss the prospects for developing crop ST via MAS. With the current advances in marker technology and a better handling of genotype by environment interaction effects, the utility of MAS for breeding for ST will gain momentum.     

Mapping of quantitative trait loci controlling seed longevity of rice (Oryza sativa L.) after various periods of seed storage

Seed longevity varies considerably in cultivated rice (Oryza sativa L.), but the underlying genetic mechanism of longevity has not been well elucidated. Quantitative trait loci (QTL) that control seed longevity after various periods of seed storage were sought using recombinant inbred lines derived from a combination involving ‘Milyang23’(Indica‐type) and ‘Akihikari’ (Japonica‐type). In all, 12 QTLs for germination and normal seedling growth were detected as indices of seed longevity on chromosome 7 (one region) and chromosome 9 (two regions) in treated seeds that had been stored under laboratory conditions for 1, 2 or 3 years.‘Milyang23’ alleles of all QTLs promoted germination and normal seedling growth after all durations of storage. These QTL regions were detected repeatedly in more than one seed condition. Therefore, we infer that these regions control seed longevity.     

Identification of quantitative trait loci underlying milling quality of rice (Oryza sativa) grains

Milling quality of rice grains is important to both producers and consumers. In this study, quantitative trait loci (QTLs) controlling brown rice rate (BR), milled rice recovery (MR) and head rice recovery (HR) were analysed by composite interval mapping over 2 years using 98 backcross inbred lines (BILs). A total of 12 QTLs for the three traits were detected, of which five were for BR, four for MR and three for HR. The proportion of phenotypic variation explained by individual QTLs ranged from 7.5 to 19.9%, and additive effects contributed by a single QTL accounted for 0.46 to 2.34% of the variation. QTL‐by‐environment interactions were observed by comparing QTL mapping of the same population grown in two consecutive years. Three of five QTLs for BR and two of four QTLs for MR were detected in 2 years, and all three QTLs for HR were detected in 1 year only. BR was significantly correlated with MR, and all four QTLs of MR were located in the same regions as those of BR. This indicated that QTLs for highly correlated traits could often be detected in the same interval.     

Genetic control of seedling tolerance to aluminum toxicity in rice

An uncomplete diallel analysis was conducted for 56 F1 progenies derived from 8 male × 7 female parents with differential Al tolerance based on root tolerance index (RTI) in a solution culture with Al concentration of 1 mM Al. Remarkable variation in RTI among the parents was observed after 6 weeks in culture. Significant (P < 0.001) general combine ability (GCA) variance for both male and female parents and specific combine ability (SCA) variance were observed. The variance of GCA was much higher than that of SCA, indicating greater additive expression of the tolerant trait. Higher narrow-sense heritability (48%) was detected, indicating the possibility of a genetic gain in selection for Al tolerance based on RTI. The tolerant performance of F1 progenies appeared to be influenced by the susceptible genotype. suggesting the inconsistent dominance effect. The possible mechanisms of the apparent inconsistent dominance was discussed in terms of the genetic background in wheat. Two restore lines, Pedel and 02428, and one sterile variety, XieqinzaoA, were found to be high in the GCA effect and SCA variance in this case. These genotypes may be useful in development of hybrid rice production on acid soils. This revised version was published online in July 2006 with corrections to the Cover Date.     

A new locus for resistance to brown planthopper identified in the indica rice variety DV85

The brown planthopper (BPH) is one of the most destructive insect pests of rice. Resistant varieties have proved to be one of the most economic and effective measures for BPH management. In this study, an indica rice ‘DV85’ showed resistance to biotype 2 of BPH by bulked seedling test, and a recombinant inbred line (RIL) population derived from a cross between a susceptible rice ‘Kinmaze’ and ‘DV85’ was phenotyped to map genetic factors conferring BPH resistance in ‘DV85′. Composite interval mapping revealed that one quantitative trait locus (QTL) with a LOD score of 10.1 was detected between XNpb202 and C1172 on chromosome 11. This QTL was designated as Qbph11. Qbph11 explained 68.4% of the phenotypic variance of BPH resistance in this population. The allele from the resistant parent ‘DV85’ at Qbph11 reduced the damage caused by BPH feeding and would be very useful in breeding resistant rice varieties via marker‐assisted selection.     

Mapping of quantitative trait loci associated with rice black‐streaked dwarf virus disease and its insect vector in rice (Oryza sativa L.)

Rice black‐streaked dwarf virus disease (RBSDVD), transmitted by small brown planthopper (SBPH, Laodelphax striatellus), causes serious loss in rice production. Breeding resistant cultivars are one of the most effective strategies to control the virus disease and its vector. By both natural inoculations in the field and modified seedling‐box screening test in the glasshouse, an indica variety WR24 showed high resistance to RBSDVD and SBPH. An F_2:3 population consisting of 153 lines derived from a cross between WR24 and a susceptible japonica variety Suyunuo was used for quantitative trait loci (QTL) analysis of RBSDVD and SBPH resistance. The linkage map consisting of 130 SSR markers was constructed with an average marker interval of 13.90 cM, spanning a total of 1890.9 cM. Totally, five QTLs for RBSDV resistance, viz. qRBSDV3^WR24, qRBSDV6^WR24, qRBSDV7^WR24, qRBSDV9^WR24 and qRBSDV11^WR24, were detected on chromosomes 3, 6, 7, 9 and 11, with LOD scores of 2.7, 3.08, 3.13, 5.28 and 3.7, respectively. Meanwhile, three QTLs for SBPH resistance, including qSBPH5^WR24, qSBPH7^WR24 and qSBPH10^WR24, were mapped on chromosomes 5, 7 and 10, with LOD scores of 2.18, 3.5 and 3.57, respectively. All resistant alleles were from WR24. Among these QTLs, qRBSDV7^WR24, qSBPH5^WR24 and qSBPH10^WR24 were newly reported, and qSBPH10^WR24 showed major effect that explained 17.9% of total phenotypic variance. The RBSDVD and SBPH resistance QTLs and the tightly linked DNA markers can be utilized in RBSDV and SBPH resistance breeding in rice.     

Identification and verification of quantitative trait loci for eating and cooking quality of rice (Oryza sativa)

This study was conducted to identify new quantitative trait loci (QTLs) that have stable effects for eating and cooking quality (ECQ) of rice. Three recombinant inbred line populations of indica rice were each planted in two years. Three traits for ECQ, amylose content (AC), gel consistency (GC) and alkali spreading value (ASV), were measured for QTL analysis. A total of 13 QTLs were detected, including four for AC, six for ASV and three for GC. Two QTLs, qGC4 in the interval RM16252–RM335 on the short arm of chromosome 4 and qGC6.2 in the Alk region, were validated in a population derived from a residual heterozygote that was homozygous at the major locus Wx. In the absence of segregation at the Wx locus, qGC4 and qGC6.2 had additive effects of 2.46 and 8.18 mm, respectively, offering a potential for improving GC property of rice varieties. Comparison between qGC4 and previous results suggests that qGC4 is likely a new QTL for GC, providing a candidate for gene cloning and functional characterization.     

Genetic analysis of salt tolerance at seedling and reproductive stages in rice (Oryza sativa)

Salinity is a major abiotic stress that limits rice production across rice areas as high‐yielding modern rice varieties are generally sensitive to salt stress. The study was conducted to deduce heritability and combining ability estimates of rice for various morphological and physiological traits using a 7 × 7 full‐diallel‐cross analysis at seedling and reproductive stages. The salinity stress treatment was 12 dS m^?1 at the seedling stage and 8 dS m^?1 at the reproductive stage. Diallel analysis revealed high for salinity tolerance scores and shoot height, moderate for shoot dry weight and root dry weight and low for Na⁺ and K⁺ concentrations and K⁺/Na⁺ ratio. The low‐to‐moderate narrow‐sense heritability for number of panicles, number of fertile spikelets, grain weight, spikelet fertility and K⁺/Na⁺ ratio suggests a large breeding population and delayed selection for tolerance until later generations. Significant maternal effects indicate that selection of the female parent is very important for desired trait development. The results of this study confirmed that salinity tolerance at the seedling and reproductive stages is regulated by a different set of genes that could be pyramided using different donors to enhance the level of tolerance.     

QTL mapping for seedling traits associated with low‐nitrogen tolerance using a set of advanced backcross introgression lines of rice

Nitrogen (N) deficiency is a major yield‐limiting factor in rice production. The objective of this study was to identify putative QTLs for low‐N stress tolerance of rice, using an advanced backcross population derived from crosses between an indica cultivar ‘93‐11’ and a japonica cultivar ‘Nipponbare’ and genotyped at 250 marker loci. Plant height, maximum root length, root dry weight, shoot dry weight and plant dry weight under two N conditions and their relative traits were used to evaluate low‐N tolerance at the seedling stage. A total of 44 QTLs were identified on chromosomes 1, 2, 3, 4, 5, 6, 8 and 9. Eight intervals on five chromosomes were identified to harbour multiple QTLs, suggesting pleiotropism or multigenic effects according to the contributor of alleles. Some QTL clusters were found in the nearby regions of genes associated with N recycling in rice, indicating that the key N metabolism genes might have effects on the expression of QTLs. Several unique QTLs for relative traits were detected, which suggested the specific genetic basis of relative performance.