Identification of quantitative trait loci associated with salt tolerance at seedling stage from Oryza rufipogon

Soil salinity is one of the major abiotic stresses affecting plant growth and crop production.In the present study,salt tolerance at rice seedling stage was evaluated using 87 introgression lines (ILs),which were derived from a cross between an elite indica cultivar Teqing and an accession of common wild rice (Oryza rufipogon Griff.).Substantial variation was observed for four traits including salt tolerance score (STS),relative root dry weight (RRW),relative shoot dry weight (RSW) and relative total dry weight (RTW).STS was significantly positively correlated with all other three traits.A total of 15 putative quantitative trait loci (QTLs) associated with these four traits were detected using single-point analysis,which were located on chromosomes 1,2,3,6,7,9 and 10 with 8％-26％ explaining the phenotypic variance.The O.rufipogon-derived alleles at 13 QTLs (86.7％) could improve the salt tolerance in the Teqing background.Four QTL clusters affecting RRW,RSW and RTW were found on chromosomes 6,7,9 and 10,respectively.Among these four QTL clusters,a major cluster including three QTLs (qRRW10,qRSW10 and qRTW10) was found near the maker RM271 on the long arm of chromosome 10,and the O.rufipogon-derived alleles at these three loci increased RRW,RSW and RTW with additive effects of 22.7％,17.3％ and 18.5％,respectively,while the phenotypic variance explained by these three individual QTLs for the three traits varied from 19％ to 26％.In addition,several salt tolerant ILs were selected and could be used for identifying and utilizing favorable salt tolerant genes from common wild rice and used in the salt tolerant rice breeding program.     

Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice

Salt tolerance was evaluated at the young seedling stage of rice (Oryza sativa L.) using recombinant inbred lines (MG RILs) from a cross between Milyang 23 (japonica/indica) and Gihobyeo (japonica). 22 of 164 MG RILs were classified as tolerant with visual scores of 3.5-5.0 in 0.7% NaCl. Interval mapping of QTLs related to salt tolerance was conducted on the basis of the visual scores at the young seedling stage. Two QTLs, qST1 and qST3, conferring salt tolerance, were detected on chromosome 1 and 3, respectively, and the total phenotypic variance explained by the two QTLs was 36.9% in the MG RIL population. qST1 was the major QTL explaining 27.8% of the total phenotypic variation. qST1 was flanked by Est12-RZ569A, and qST3 was flanked by RG179-RZ596. The detection of new QTLs associated with salt tolerance will provide important information for the functional analysis of rice salt tolerance.     

Identification of quantitative trait loci for cadmium tolerance and accumulation in wheat

Quantitative trait loci (QTL) for Cadmium (Cd) tolerance and accumulation in wheat (Triticum aestivum L.) were identified, using 103 recombinant inbred lines (RILs) derived from a cross of Ch × Sh at germination and seedling stages. The traits of germination, growth and physiology were measured. Cd tolerance indexes (TI) were calculated for plants under Cd stress relative to control conditions. Cd concentrations in both root and shoot were determined and the amount of Cd accumulation and translocation calculated. The phenotypic variation of the above traits showed a continuous distribution pattern among the RILs. Twenty-six QTLs were detected, (16 of which were designated for the traits under the control and Cd stress, 8 for Cd tolerance and 2 for root Cd accumulation). These 26 QTLs individually could explain 7.97–60.16% of the phenotypic variation. Fourteen QTLs were positive (with the additive effects coming from Ch) while the remaining 12 QTLs were negative (with the additive effects contributed by Sh). No QTL were detected in the same region on the chromosomes of wheat. The results indicated that genetic mechanisms controlling the traits of Cd tolerance were independent from each other. Therefore, in this study, the properties of Cd tolerance and accumulation showed to be independent traits in wheat.     

Identification of quantitative trait loci and associated candidate genes for low-temperature tolerance in cold-hardy winter wheat

Low-temperature (LT) tolerance is an important economic trait in winter wheat (Triticum aestivum L.) that determines the plants’ ability to cope with below freezing temperatures. Essential elements of the LT tolerance mechanism are associated with the winter growth habit controlled by the vernalization loci (Vrn-1) on the group 5 chromosomes. To identify genomic regions, which in addition to vrn-1 determine the level of LT tolerance in hexaploid wheat, two doubled haploid (DH) mapping populations were produced using parents with winter growth habit (vrn-A1, vrn-B1, and vrn-D1) but showing different LT tolerance levels. A total of 107 DH lines were analyzed by genetic mapping to produce a consensus map of 2,873 cM. The LT tolerance levels for the Norstar (LT₅₀=−20.7°C) × Winter Manitou (LT₅₀=−14.3°C) mapping population ranged from −12.0 to −22.0°C. Single marker analysis and interval mapping of phenotyped lines revealed a major quantitative trait locus (QTL) on chromosome 5A and a weaker QTL on chromosome 1D. The 5A QTL located 46 cM proximal to the vrn-A1 locus explained 40% of the LT tolerance variance. Two C-repeat Binding Factor (CBF) genes expressed during cold acclimation in Norstar were located at the peak of the 5A QTL.     

Identification of quantitative trait loci for race-nonspecific resistance to tan spot in wheat

Tan spot, caused by Pyrenophora tritici-repentis (Ptr), is an economically important foliar disease in the major wheat growing areas throughout the world. Multiple races of the pathogen have been characterized based on their ability to cause necrosis and/or chlorosis on differential wheat lines. In this research, we evaluated a population of recombinant inbred lines derived from a cross between the common wheat varieties Grandin and BR34 for reaction to tan spot caused by Ptr races 1–3 and 5. Composite interval mapping revealed QTLs on the short arm of chromosome 1B and the long arm of chromosome 3B that were significantly associated with resistance to all four races. The effects of the two QTLs varied for the different races. The 1B QTL explained from 13% to 29% of the phenotypic variation, whereas the 3B QTL explained from 13% to 41% of the variation. Additional minor QTLs were detected but not associated with resistance to all races. The host-selective toxin Ptr ToxA, which is produced by races 1 and 2, was not a significant factor in the development of disease in this population. The race-nonspecific resistance derived from BR34 may take precedence over the gene-for-gene interaction known to be associated with the wheat–Ptr system.     

Identification of quantitative trait loci associated with self-compatibility in a Prunus species

Self-compatibility in Rosaceous fruit species is based on a single-locus qualitative trait. However, the evidence observed in different species has indicated the presence of modifier genes outside the S locus affecting the expression of self-compatibility/self-incompatibility. The study of a progeny obtained from the cross of the almond genotypes ‘Vivot’× ‘Blanquerna’ has allowed the construction of a genetic map based on microsatellite markers and the identification for the first time in the Rosaceae family of two additional loci located outside the S locus and affecting the expression of self-compatibility/self-incompatibility. A quantitative trait locus (QTL) was located relatively close to the S locus, on linkage group 6 (G6), whereas the second one was located on G8. These QTLs appear to be involved in conferring self-compatibility to genotypes not possessing the S _f allele. These results are consistent with almond being a self-incompatible species with a genetic background of pseudo-self-compatibility controlled by modifier genes. The effect of the S _f allele and the two QTLs may contribute to explain the wide range of fruit sets observed when self-pollinating different almond genotypes.     

Genomic distribution of quantitative trait loci for yield and yield-related traits in common wheat

A major objective of quantitative trait locus(QTL)studies is to find genes/markers that can be used in breeding programs via marker assisted selection(MAS).We surveyed the QTLs for yield and yield related traits and their genomic distributions in common wheat(Triticum aestivum L.)in the available published reports.We then carried out a meta-QTL(MQTL)analysis to identify the major and consistent QTLs for these traits.In total,55 MQTLs were identified,of which 12 significant MQTLs were located on wheat chromosomes 1A,1B,2A,2D,3B,4A,4B,4D and 5A.Our study showed that the genetic control of yield and its components in common wheat involved the important genes such as Rht and Vrn.Furthermore,several significant MQTLs were found in the chromosomal regions corresponding to several rice genomic locations containing important QTLs for yield related traits.Our results demonstrate that meta-QTL analysis is a powerful tool for confirming the major and stable QTLs and refining their chromosomal positions in common wheat,which may be useful for improving the MAS efficiency of yield related traits.     

Detection of quantitative trait loci associated with leaf rust resistance in bread wheat.

Leaf rust, caused by Puccinia recondita Rob. ex Desm., is a common disease in wheat. The objective of this study was to develop molecular markers associated with the quantitative trait loci (QTLs) putatively conferring durable leaf rust resistance in Triticum aestivum L. em. Thell. A population of 77 recombinant inbred lines (RILs) developed from 'Parula' (resistant) and 'Siete Cerros' (moderately susceptible) was used. Bulked segregant analysis was done using random amplified polymorphic DNAs (RAPDs) with DNA enriched for low-copy sequences using hydroxyapatite chromatography. Out of 400 decamer primers screened, 3 RAPD markers were identified between the bulk of the most resistant and the bulk of the most susceptible lines. These were cloned and used as probes on the RILs in Southern hybridizations. Two probes revealed two tightly linked loci. One-way analysis of variance showed that these two loci, and another revealed by the third probe, were linked to QTLs controlling leaf rust resistance based on data taken from 2 years of replicated field trials. Cytogenetic analysis placed the two tightly linked loci on the long arm of chromosome 7B. The third probe detected loci located on the short arms of chromosomes 1B and 1D. It is suggested that the QTL detected on 7BL may well be homoeoallelic to Lr34.     

Identification of quantitative trait loci controlling gene expression during the innate immunity response of soybean

Microbe-associated molecular pattern-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. However, most of our knowledge of MTI comes from studies of model systems with relatively little work done with crop plants. In this work, we report on variation in both the microbe-associated molecular pattern-triggered oxidative burst and gene expression across four soybean (Glycine max) genotypes. Variation in MTI correlated with the level of pathogen resistance for each genotype. A quantitative trait locus analysis on these traits identified four loci that appeared to regulate gene expression during MTI in soybean. Likewise, we observed that both MTI variation and pathogen resistance were quantitatively inherited. The approach utilized in this study may have utility for identifying key resistance loci useful for developing improved soybean cultivars.     

Mapping quantitative trait loci associated with root penetration ability of wheat in contrasting environments

The aim of this research was to investigate the genetic basis for variation in root penetration ability and associated traits in the mapping population derived from the Australian bread wheat cultivars Halberd and Cranbrook in soil columns containing wax layers grown in controlled conditions and to compare this with performance in the field. Root and shoot traits of the doubled haploid line (DHL) from a cross of Halberd and Cranbrook were evaluated in soil columns containing wax layers. Contrasting DHLs that varied in the ability to penetrate a wax layer in soil columns were then evaluated for maximum root depth in the field on contrasting soils at Merredin, Western Australia. Genetic control was complex, and numerous quantitative trait loci (QTL) (53 in total) were located across most chromosomes that had a small genetic effect (LOD scores of 3.2–9.1). Of these QTL, 29 were associated with root traits, 37 % of which were contributed positively by the Halberd with key traits being located on chromosomes 2D, 4A, 6B, and 7B. Variation in root traits of DHL in soil columns was linked with field performance. Despite the complexity of the traits and a large number of small QTL, the results can be potentially used to explore allelic diversity in root traits for hardpan penetration.     

Mapping and validation of quantitative trait loci associated with wheat yellow mosaic bymovirus resistance in bread wheat

Wheat yellow mosaic (WYM) caused by wheat yellow mosaic bymovirus (WYMV) has been growing as one of the most serious diseases affecting wheat production in China. In this study, the association of quantitative trait loci (QTLs) governing WYMV resistance with molecular markers was established using 164 recombinant inbred lines (RILs) derived from 'Xifeng Wheat' (highly resistant)?×?'Zhen 9523' (highly susceptible). Phenotypic data of WYMV resistance of the RILs were collected from 4-year, two-location replicated field trials. A molecular marker-based linkage map, which was comprised of 273 non-redundant loci and represented all the 21 wheat chromosomes, was constructed with the JoinMap 4.0 software. Using the Windows QTL Cartographer V2.5 software, three QTLs associated with WYMV resistance, QYm.njau-3B.1, QYm.njau-5A.1 and QYm.njau-7B.1, were detected on chromosomes 3BS, 5AL, and 7BS, respectively. The favorable allele effects were all contributed by 'Xifeng Wheat'. Among the three QTLs, QYm.njau-3B.1 and QYm.njau-5A.1 were detected in all the four trials and the overall mean, and could explain 3.3-10.2% and 25.9-53.7% of the phenotypic variation, respectively, while QYm.njau-7B.1 was detected in one trial and the overall mean and explained 4.9 and 3.3% of the phenotypic variation, respectively. A large portion of the variability for WYMV response was explained by a major QTL, QYm.njau-5A.1. The relationship of the molecular markers linked with QYm.njau-5A.1 and the WYMV resistance was further validated using a secondary F(2) population. The results showed that three markers, i.e., Xwmc415.1, CINAU152, and CINAU153, were closely linked to QYm.njau-5A.1 with the genetic distances of 0.0, 0.0, and 0.1?cM, respectively, indicating they should be useful in marker-assisted selection (MAS) wheat breeding for WYMV resistance. A panel of germplasm collection consisting of 46 wheat varieties with known WYMV response phenotypes was further used to validate the presence and effects of QYm.njau-5A.1 and the above three markers. It was found that QYm.njau-5A.1 was present in 12 of the 34 WYMV-resistant varieties.     

Quantitative trait loci associated with drought tolerance at reproductive stage in rice

Drought is a major constraint to rice (Oryza sativa) yield and its stability in rainfed and poorly irrigated environments. Identifying genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and development of more drought tolerant cultivars. Quantitative trait loci (QTL) for grain yield and its components and other agronomic traits were identified using a subset of 154 doubled haploid lines derived from a cross between two rice cultivars, CT9993-510 to 1-M and IR62266-42 to 6-2. Drought stress treatments were managed by use of a line source sprinkler irrigation system, which provided a linearly decreasing level of irrigation coinciding with the sensitive reproductive growth stages. The research was conducted at the Ubon Rice Research Center, Ubon, Thailand. A total of 77 QTL were identified for grain yield and its components under varying levels of water stress. Out of the total of 77 QTL, the number of QTL per trait were: 7-grain yield (GY); 8-biological yield (BY); 6-harvest index (HI); 5-d to flowering after initiation of irrigation gradient (DFAIG); 10-total spikelet number (TSN); 7-percent spikelet sterility (PSS); 23-panicle number (PN); and 11-plant height (PH). The phenotypic variation explained by individual QTL ranged from 7.5% to 55.7%. Under well-watered conditions, we observed a high genetic association for BY, HI, DFAIG, PSS, TSN, PH, and GY. However, only BY and HI were found to be significantly associated with GY under drought treatments. QTL flanked by markers RG104 to RM231, EMP2_2 to RM127, and G2132 to RZ598 on chromosomes 3, 4, and 8 were associated with GY, HI, DFAIG, BY, PSS, and PN under drought treatments. The aggregate effects of these QTL on chromosomes 3, 4, and 8 resulted in higher grain yield. These QTL will be useful for rainfed rice improvement, and will also contribute to our understanding of the genetic control of GY under drought conditions at the sensitive reproductive stage. Close linkage or pleiotropy may be responsible for the coincidence of QTL detected in this experiment. Digenic interactions between QTL main effects for GY, BY, HI, and PSS were observed under irrigation treatments. Most (but not all) DH lines have the same response in measure of productivity when the intensity of water deficit was increased, but no QTL by irrigation treatment interaction was detected. The identification of genomic regions associated with GY and its components under drought stress will be useful for marker-based approaches to improve GY and its stability for farmers in drought-prone rice environments.     

Mapping of quantitative trait loci associated with protein expression variation in barley grains

Barley (Hordeum vulgare) is an important cereal crop grown for both the feed and malting industries. Hence, there is great interest to gain deeper insight into the determinants of grain nutritional quality in order to improve the assessment of new traits. Two-dimensional gel electrophoresis was employed for the characterization of the grain proteome of doubled-haploid introgression lines (IL) representing a wild barley genome (Hordeum spontaneum Hs213) within a modern cultivar background (H. vulgare cv. Brenda). Proteome maps were subjected to differential cluster analysis and revealed ILs with similar or different protein expression patterns compared to the Brenda parent. A total of 51 quantitative trait loci for protein expression (pQTL) were detected, and proteins underlying these pQTL were further examined by mass spectrometry. Identification was successful for 49 of the segregating spots and functional annotation of proteins revealed that most proteins are involved in metabolism and disease/defence-related processes. Among those, multigene families of glyceraldehyde-3-phosphate dehydrogenases, heat shock proteins, peroxidases, and serpins were identified. Overall, eight pQTL signals were discovered in two independently grown sets of plants. The mapped spots included protein disulfide isomerase, α-amylase inhibitor BDAI, NADP malic enzyme, adenosine kinase and peroxidase BP1. Specific marker information of proteins involved in developmental events and protein storage as well as in disease- and defence-related processes now allows for targeted breeding approaches to improve the grain quality in barley.     

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.     

Identification of major quantitative trait loci for root diameter in synthetic hexaploid wheat under phosphorus-deficient conditions

Synthetic hexaploid wheat (SHW) possesses numerous genes for resistance to stress, including phosphorus (P) deficiency. Root diameter (RDM) plays an important role in P-deficiency tolerance, but information related to SHW is still limited. Thus, the objective of this study was to investigate the genetic architecture of RDM in SHW under P-deficient conditions. To this end, we measured the RDM of 138 F₉ recombinant inbred lines derived from an F₂ population of a synthetic hexaploid wheat line (SHW-L1) and a common wheat line (Chuanmai32) under two P conditions, P sufficiency (PS) and P deficiency (PD), and mapped quantitative trait loci (QTL) for RDM using an enriched high-density genetic map, containing 120,370 single nucleotide polymorphisms, 733 diversity arrays technology markers, and 119 simple sequence repeats. We identified seven RDM QTL for P-deficiency tolerance that individually explained 11–14.7% of the phenotypic variation. Five putative candidate genes involved in root composition, energy supply, and defense response were predicted. Overall, our results provided essential information for cloning genes related to P-deficiency tolerance in common wheat that might help in breeding P-deficiency-tolerant wheat cultivars.     

Quantitative trait loci associated with seed and seedling traits in Lactuca

Seed and seedling traits related to germination and stand establishment are important in the production of cultivated lettuce (Lactuca sativa L.). Six seed and seedling traits segregating in a L. sativa cv. Salinas x L. serriola recombinant inbred line population consisting of 103 F8 families revealed a total of 17 significant quantitative trait loci (QTL) resulting from three seed production environments. Significant QTL were identified for germination in darkness, germination at 25 and 35°C, median maximum temperature of germination, hypocotyl length at 72 h post-imbibition, and plant (seedling) quality. Some QTL for germination and early seedling growth characteristics were co-located, suggestive of pleiotropic loci regulating these traits. A single QTL (Htg6.1) described 25 and 23% of the total phenotypic variation for high temperature germination in California- and Netherlands-grown populations, respectively, and was significant between 33 and 37°C. Additionally, Htg6.1 showed significant epistatic interactions with other Htg QTL and a consistent effect across all the three seed production environments. L. serriola alleles increased germination at these QTL. The estimate of narrow-sense heritability (h²) of Htg6.1 was 0.84, indicating potential for L. serriola as a source of germination thermotolerance for lettuce introgression programs.