Using QTL mapping to investigate the relationships between abiotic stress tolerance (drought and salinity) and agronomic and physiological traits

Background

Drought and salinity are two major abiotic stresses that severely limit barley production worldwide. Physiological and genetic complexity of these tolerance traits has significantly slowed the progress of developing stress-tolerant cultivars. Marker-assisted selection (MAS) may potentially overcome this problem. In the current research, seventy two double haploid (DH) lines from a cross between TX9425 (a Chinese landrace variety with superior drought and salinity tolerance) and a sensitive variety, Franklin were used to identify quantitative trait loci (QTL) for drought and salinity tolerance, based on a range of developmental and physiological traits.

Results

Two QTL for drought tolerance (leaf wilting under drought stress) and one QTL for salinity tolerance (plant survival under salt stress) were identified from this population. The QTL on 2H for drought tolerance determined 42% of phenotypic variation, based on three independent experiments. This QTL was closely linked with a gene controlling ear emergency. The QTL on 5H for drought tolerance was less affected by agronomic traits and can be effectively used in breeding programs. A candidate gene for this QTL on 5H was identified based on the draft barley genome sequence. The QTL for proline accumulation, under both drought and salinity stresses, were located on different positions to those for drought and salinity tolerance, indicating no relationship with plant tolerance to either of these stresses.

Conclusions

Using QTL mapping, the relationships between QTL for agronomic and physiological traits and plant drought and salinity tolerance were studied. A new QTL for drought tolerance which was not linked to any of the studied traits was identified. This QTL can be effectively used in breeding programs. It was also shown that proline accumulation under stresses was not necessarily linked with drought or salinity tolerance based on methods of phenotyping used in this experiment. The use of proline content in breeding programs can also be limited by the accuracy of phenotyping.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1243-8) contains supplementary material, which is available to authorized users.     

Quantitative trait loci controlling barley powdery mildew and scald resistances in two different barley doubled haploid populations

Powdery mildew and scald can cause significant yield loss in barley. In order to identify new resistance genes for powdery mildew and scald in barley, two barley doubled haploid (DH) populations were screened for adult plant resistance in the field and glasshouse under natural infection. The mapping populations included 92 DH lines from the cross of TX9425 × Franklin and 177 DH lines from the cross of Yerong × Franklin. Two quantitative trait loci (QTL) for resistance to powdery mildew were identified in the TX9425 × Franklin population. These QTL were mapped to chromosomes 7H and 5H, respectively. The phenotypic variation explained by the two QTL detected in this population was 22 and 17%, respectively. Three significant QTL were identified from the Yerong × Franklin population for the resistance to powdery mildew; the major one, detected on the short arm of chromosome 1H, explained 66% of phenotypic variation. The major QTL for scald resistance, identified from two different populations which shared a common parent, Franklin, were mapped in the similar position on 3H. However, the Franklin allele provided resistance to one population but susceptibility to the other population. The Yerong allele on 3H showed much better resistance to scald than the Franklin allele, which has not been reported before. Using high-density maps for both populations, some markers which were very close to the resistance genes were identified. Transgression beyond the parents in disease resistances of the DH populations indicates that both small-effect QTLs and genetic background may also have significant contributions towards the resistance.     

QTL mapping of chromosomal regions conferring reproductive frost tolerance in barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.)

Spring radiation frost is a major abiotic stress in southern Australia, reducing yield potential and grain quality of barley by damaging sensitive reproductive organs in the latter stages of development. Field-based screening methods were developed, and genetic variation for reproductive frost tolerance was identified. Mapping populations that were segregating for reproductive frost tolerance were screened and significant QTL identified. QTL on chromosome 2HL were identified for frost-induced floret sterility in two different populations at the same genomic location. This QTL was not associated with previously reported developmental or stress-response loci. QTL on chromosome 5HL were identified for frost-induced floret sterility and frost-induced grain damage in all three of the populations studied. The locations of QTL were coincident with previously reported vegetative frost tolerance loci close to the vrn-H1 locus. This locus on chromosome 5HL has now been associated with response to cold stress at both vegetative and reproductive developmental stages in barley. This study will allow reproductive frost tolerance to be seriously pursued as a breeding objective by facilitating a change from difficult phenotypic selection to high-throughput genotypic selection.     

A Single Locus Is Responsible for Salinity Tolerance in a Chinese Landrace Barley (Hordeum vulgare L.)

Introduction

Salinity and waterlogging are two major abiotic stresses severely limiting barley production. The lack of a reliable screening method makes it very hard to improve the tolerance through breeding programs.

Methods

This work used 188 DH lines from a cross between a Chinese landrace variety, TX9425 (waterlogging and salinity tolerant), and a Japanese malting barley, Naso Nijo (waterlogging and salinity sensitive), to identify QTLs associated with the tolerance.

Results

Four QTLs were found for waterlogging tolerance. The salinity tolerance was evaluated with both a hydroponic system and in potting mixture. In the trial with potting mixture, only one major QTL was identified to associate with salinity tolerance. This QTL explained nearly 50% of the phenotypic variation, which makes it possible for further fine mapping and cloning of the gene. This QTL was also identified in the hydroponic experiment for different salt-related traits. The position of this QTL was located at a similar position to one of the major QTLs for waterlogging tolerance, indicating the possibility of similar mechanisms controlling both waterlogging and salinity tolerance.

Conclusion

The markers associated with the QTL provided a unique opportunity in breeding programs for selection of salinity and waterlogging tolerance.     

Variation in feed quality traits for beef cattle in Steptoe?×?Morex barley population

Barley is a major feed source for livestock in the western regions of North America. Feed quality of beef cattle has been neglected as a selection criterion because of lack of understanding of the feed characteristics that could be responsive to selection and would improve feedlot performance. A Steptoe × Morex population was planted in irrigated and rain-fed environments, and collected data were used to evaluate the genetic variation in dry matter and starch digestibilities, acid detergent fiber, protein and starch contents, and to map quantitative trait loci controlling the variation in these traits. Transgressive genotypes indicate the wide genetic variation of these traits. High heritability estimates for these traits suggest that early selection for these traits during breeding would be achievable. A total of 32 main effect QTL and five epistatic QTL were identified which conditioned feed traits on different barley chromosomes. QTL for acid detergent fiber and starch contents overlapped on chromosome 6H at the Nar7 locus. Tight negative correlation between the two traits suggest the usability of Nar7 as anchor marker in marker-assisted selection programs to develop barley with low acid detergent fiber and high starch content.     

Identifying a Major QTL Associated with Salinity Tolerance in Nile Tilapia Using QTL-Seq

Selection of new lines with high salinity tolerance allows for economically feasible production of tilapias in brackish water areas. Mapping QTLs and identifying the markers linked to salinity-tolerant traits are the first steps in the improvement of the tolerance in tilapia through marker-assisted selection techniques. By using QTL-seq strategy and linkage-based analysis, two significant QTL intervals (chrLG4 and chrLG18) on salinity-tolerant traits were firstly identified in the Nile tilapia. Fine mapping with microsatellite and SNP markers suggested a major QTL region that located at 23.0 Mb of chrLG18 and explained 79% of phenotypic variation with a LOD value of 95. Expression analysis indicated that at least 10 genes (e.g., LACTB2, KINH, NCOA2, DIP2C, LARP4B, PEX5R, and KCNJ9) near or within the QTL interval were significantly differentially expressed in intestines, brains, or gills under 10, 15, or 20 ppt challenges. Our findings suggest that QTL-seq can be effectively utilized in QTL mapping of salinity-tolerant traits in fish. The identified major QTL is a promising locus to improve our knowledge on the genetic mechanism of salinity tolerance in tilapia.     

Quantitative Trait Loci for Salinity Tolerance Identified under Drained and Waterlogged Conditions and Their Association with Flowering Time in Barley (Hordeum vulgare. L)

Introduction

Salinity is one of the major abiotic stresses affecting crop production via adverse effects of osmotic stress, specific ion toxicity, and stress-related nutritional disorders. Detrimental effects of salinity are also often exacerbated by low oxygen availability when plants are grown under waterlogged conditions. Developing salinity-tolerant varieties is critical to overcome these problems, and molecular marker assisted selection can make breeding programs more effective.

Methods

In this study, a double haploid (DH) population consisting of 175 lines, derived from a cross between a Chinese barley variety Yangsimai 1 (YSM1) and an Australian malting barley variety Gairdner, was used to construct a high density molecular map which contained more than 8,000 Diversity Arrays Technology (DArT) markers and single nucleotide polymorphism (SNP) markers. Salinity tolerance of parental and DH lines was evaluated under drained (SalinityD) and waterlogged (SalinityW) conditions at two different sowing times.

Results

Three quantitative trait loci (QTL) located on chromosome 1H, single QTL located on chromosomes 1H, 2H, 4H, 5H and 7H, were identified to be responsible for salinity tolerance under different environments. Waterlogging stress, daylight length and temperature showed significant effects on barley salinity tolerance. The QTL for salinity tolerance mapped on chromosomes 4H and 7H, QSlwd.YG.4H, QSlwd.YG.7H and QSlww.YG.7H were only identified in winter trials, while the QTL on chromosome 2H QSlsd.YG.2H and QSlsw.YG.2H were only detected in summer trials. Genes associated with flowering time were found to pose significant effects on the salinity QTL mapped on chromosomes 2H and 5H in summer trials. Given the fact that the QTL for salinity tolerance QSlsd.YG.1H and QSlww.YG.1H-1 reported here have never been considered in the literature, this warrants further investigation and evaluation for suitability to be used in breeding programs.     

Modeling uptake of cadmium from solution outside of root to cell wall of shoot in rice seedling

Barley (Hordeum vulgare L.) is well known for its relatively high salt tolerance among cereal crops. However, the genetic variation of cultivated barley becomes narrower due to continuous artificial selection and breeding processes. Compared with cultivated barley, wild barley contains wider genetic variation and abundant sources for abiotic stress tolerance, considering as an elite resource for mechanism study on salt tolerance. In this study, Tibetan wild barley accession XZ113 identified with high salt tolerance, was used to investigate ionic responses and to identify proteins involved in salt tolerance in roots and shoots at early stage of salt stress, during 48 h. Exposed to salinity, shoot growth is more sensitive than root growth. Conversely, K/Na ratio in the shoots was larger than that in the roots, and both were above 1.0. Steady-state K⁺ flux experiment showed XZ113 had a strong K⁺-retaining ability under salt stress, maybe contributing to its good performance of the absolute growth rate. Proteomic results suggested that monodehydroascorbate reductase and peroxidases related to reactive oxygen species scavenging in the roots and phosphoglycerate kinase, triosephosphate isomerase and sedoheptulose-1,7-bisphosphatase associated with photosynthesis and metabolisms in the shoots, played important roles in salt tolerance at early stage of salinity in wild barley.     

Identification of QTLs with main, epistatic and QTL?×?environment interaction effects for salt tolerance in rice seedlings under different salinity conditions

Salt tolerance of rice (Oryza sativa L.) at the seedling stage is one of the major determinants of its stable establishment in saline soil. One population of recombinant inbred lines (RILs, F (2:9)) derived from a cross between the salt-tolerant variety Jiucaiqing and the salt-sensitive variety IR26 was used to determine the genetic mechanism of four salt tolerance indices, seedling height (SH), dry shoot weight (DSW), dry root weight (DRW) and Na/K ratios (Na/K) in roots after 10 days in three salt concentrations (0.0, 0.5 and 0.7 % NaCl). The main effect QTLs (M-QTLs) and epistatic QTLs (E-QTLs) were detected by QTL IciMapping program using single environment phenotypic values. Eleven M-QTLs and 11 E-QTLs were identified for the salt tolerance indices. There were six M-QTLs and two E-QTLs identified for SH, three M-QTLs and five E-QTLs identified for DSW, two M-QTLs and one E-QTL identified for DRW, and three E-QTLs identified for Na/K. The phenotypic variation explained by each M-QTL and E-QTL ranged from 7.8 to 23.9 % and 13.3 to 73.7 %, respectively. The QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values. Six M-QTLs and five E-QTLs were identified. The phenotypic variation explained by each QTL and QTL × environment interaction ranged from 0.95 to 6.90 % and 0.02 to 0.50 %, respectively. By comparing chromosomal positions of these M-QTLs with those previously identified, five M-QTLs qSH1.3, qSH12.1, qSH12.2, qDSW12.1 and qDRW11 might represent novel salt tolerance genes. Five selected RILs with high salt tolerance had six to eight positive alleles of the M-QTLs, indicating that pyramiding by marker-assisted selection (MAS) of M-QTLs can be applied in rice salt tolerance breeding programs.     

A quantitative trait locus for long photoperiod response mapped on chromosome 4H in barley

Photoperiod response is a key determinant for barley adaptation to diverse environments. A major quantitative trait locus (QTL) for response to long photoperiod was identified in Australia (Perth, 31°56??S) and China (Wuhan, 30°33??N) using 178 doubled haploid lines derived from a cross of an Australian barley, Baudin, and a Canadian barley, AC Metcalfe. The QTL was detected as a major QTL in the 18-h photoperiod glasshouse experiments and mapped to the Xp12m50B199?CXp13m47B399 interval on chromosome 4H with a LOD score of 57 in Australia and confirmed in China. The single QTL accounted for 77.48 and 37.81% of phenotypic variation for long photoperiod response in Australia and China, respectively. The same QTL also controlled heading date in Australia, under normal and extended photoperiod conditions, and in China, under extended photoperiod and late-sown conditions. The QTL advanced heading date by 27.8?days in Australia and 42.5?days in China under a 18-h photoperiod. In addition, QTL for heading date were identified on chromosomes 2H and 3H. The chromosome 3H QTL was associated with the denso gene and detected in all conditions, but the chromosome 2H QTL was only detected in Australia. The new photoperiod response QTL, Qhea.BM.4-13/Qpho.BM.4-13, on chromosome 4H and its associated markers will provide an alternative for plant breeders developing new varieties for different environments using marker-assisted selection.     

Genetic dissection of grain beta-glucan and amylose content in barley (Hordeum vulgare L.)

High beta-glucan (BG) barleys (Hordeum vulgare L.) have major potential as food ingredients due to their well-known health benefits. Quantitative trait loci (QTL) associated with BG have been reported in traditional barley varieties with intermediate levels of BG, but no QTL studies have been reported in hull-less barley varieties with high BG levels. In this study, QTL analysis was performed to identify markers linked to high BG and amylose in the hull-less barley varieties Falcon (4–5 % BG) and Azhul (8–9 % BG) using a newly developed recombinant inbred line (RIL) mapping population. The population was grown over 3 years (2007–2009) at sites in Yuma, AZ, USA; Leeston, New Zealand; Aberdeen, ID, USA; and Tetonia, ID, USA. We identified 17 QTL associated with either BG or amylose content. QTL contributing to high BG were located on chromosomes 3H, 4H, 5H, 6H and 7H, while QTL contributing to amylose were located on chromosomes 1H, 5H and 7H. Additionally, we identified QTL affecting both BG and amylose content located on chromosomes 1H and 7H. Transgressive segregation was observed in some of the RILs and exceptions were discovered contradicting an inverse relationship between BG and amylose. This work will provide the basis for gene cloning and marker-assisted selection in combination with traditional field selection to improve barley breeding for high BG content.     

Photosynthetic capacity is related to the cellular and subcellular partitioning of Na+, K+ and Cl- in salt-affected barley and durum wheat

The capacity of plants to tolerate high levels of salinity depends on the ability to exclude salt from the shoot, or to tolerate high concentrations of salt in the leaf (tissue tolerance). It is widely held that a major component of tissue tolerance is the capacity to compartmentalize salt into safe storage places such as vacuoles. This mechanism would avoid toxic effects of salt on photosynthesis and other key metabolic processes. To test this, the relationship between photosynthetic capacity and the cellular and subcellular distribution of Na+, K+ and Cl- was studied in salt-sensitive durum wheat (cv. Wollaroi) and salt-tolerant barley (cv. Franklin) seedlings grown in a range of salinity treatments. Photosynthetic capacity parameters (Vcmax, Jmax) of salt-stressed Wollaroi decreased at a lower leaf Na+ concentration than in Franklin. Vacuolar concentrations of Na+, K+ and Cl- in mesophyll and epidermal cells were measured using cryo-scanning electron microscopy (SEM) X-ray microanalysis. In both species, the vacuolar Na+ concentration was similar in mesophyll and epidermal cells, whereas K+ was at higher concentrations in the mesophyll, and Cl- higher in the epidermis. The calculated cytoplasmic Na+ concentration increased to higher concentrations with increasing bulk leaf Na+ concentration in Wollaroi compared to Franklin. Vacuolar K+ concentration was lower in the epidermal cells of Franklin than Wollaroi, resulting in higher cytoplasmic K+ concentrations and a higher K+ : Na+ ratio. This study indicated that the maintenance of photosynthetic capacity (and the resulting greater salt tolerance) at higher leaf Na+ levels of barley compared to durum wheat was associated with the maintenance of higher K+, lower Na+ and the resulting higher K+ : Na+ in the cytoplasm of mesophyll cells of barley.     

A major QTL controlling the tolerance to manganese toxicity in barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.)

Waterlogging stress disturbs plant metabolism through increased ion (manganese and iron) toxicity resulting from the changes in the soil redox potential under hypoxic conditions. Our previous study found a significant correlation between the tolerance to Mn²⁺ toxicity and waterlogging stress tolerance in barley, suggesting that waterlogging tolerance could be increased by improving the tolerance to Mn²⁺ toxicity. In this study, a doubled-haploid (DH) population from the cross between barley varieties Yerong and Franklin (waterlogging-tolerant and -sensitive, respectively) was used to identify QTL controlling tolerance to Mn²⁺ toxicity based on chlorophyll content and plant survival as selection criteria. Four significant QTL for plant survival under Mn²⁺ stress (QSur.yf.1H, QSur.yf.3H, QSur.yf.4H, and QSur.yf.6H) were identified in this population at the seedling stage. Two significant QTL (QLC.yf.3H and QLC.yf.6H) controlling leaf chlorosis under Mn²⁺ stress were identified on chromosomes 3H and 6H close to QSur.yf.3H and QSur.yf.6H. The major QTL QSur.yf.3H, located near the marker Bmag0013, explained 21% of the phenotypic variation. The major QTL for plant survival on 3H was validated in a different DH population (TX9425/Naso Nijo). This major QTL could potentially be used in breeding programmes to enhance tolerance to both manganese toxicity and waterlogging.     

Halophyte Improvement for a Salinized World

It is more important to improve the salt tolerance of crops in a salinized world with the situations of increasing populations, declining crop yields, and a decrease in agricultural lands. Attempts to produce salt-tolerant crops have involved the manipulation of existing crops through conventional breeding, genetic engineering and marker-assisted selection (MAS). However, these have, so far, not produced lines growing on highly saline water. Hence, the domestication of wild halophytes as crops appears to be a feasible way to develop agriculture in highly saline environments. In this review, at first, the assessment criteria of salt tolerance for halophytes are discussed. The traditional criteria for the classification of salinity in crops are less applicable to strong halophytes with cubic growth curves at higher salinities. Thus, realistic assessment criteria for halophytes should be evaluated at low and high salinity levels. Moreover, absolute growth rather than relative growth in fields during a crop's life cycle should be considered. Secondly, the use of metabolomics to understand the mechanisms by which halophytes respond to salt tolerance is highlighted as is the potential for metabolomics-assisted breeding of this group of plants. Metabolomics provides a better understanding of the changes in cellular metabolism induced by salt stress. Identification of metabolic quantitative trait loci (QTL) associated with salt tolerance might provide a new method to aid the selection of halophyte improvement. Thirdly, the identification of germplasm-regression-combined (GRC) marker-trait association and its potential to identifying markers associated with salt tolerance is outlined. Results of MAS/linkage map-QTL have been modest because of the absence of QTLs with tight linkage, the non-availability of mapping populations and the substantial time needed to develop such populations. To overcome these limitations, identification by GRC-based marker-trait association has been successfully applied to many plant traits, including salt tolerance. Finally, we provide a prospect on the challenges and opportunities for halophyte improvement, especially in the integration of metabolomics- and GRC-marker-assisted selection towards new or unstudied halophyte breeding, for which no other genetic information, such as linkage maps and QTL, are available.     

Identification of a major QTL allele from wild soybean (Glycine soja Sieb. & Zucc.) for increasing alkaline salt tolerance in soybean

Salt-affected soils are generally classified into two main categories, sodic (alkaline) and saline. Our previous studies showed that the wild soybean accession JWS156-1 (Glycine soja) from the Kinki area of Japan was tolerant to NaCl salt, and the quantitative trait locus (QTL) for NaCl salt tolerance was located on soybean linkage group N (chromosome 3). Further investigation revealed that the wild soybean accession JWS156-1 also had a higher tolerance to alkaline salt stress. In the present study, an F₆ recombinant inbred line mapping population (n = 112) and an F₂ population (n = 149) derived from crosses between a cultivated soybean cultivar Jackson and JWS156-1 were used to identify QTL for alkaline salt tolerance in soybean. Evaluation of soybean alkaline salt tolerance was carried out based on salt tolerance rating (STR) and leaf chlorophyll content (SPAD value) after treatment with 180 mM NaHCO₃ for about 3 weeks under greenhouse conditions. In both populations, a significant QTL for alkaline salt tolerance was detected on the molecular linkage group D2 (chromosome 17), which accounted for 50.2 and 13.0% of the total variation for STR in the F₆ and the F₂ populations, respectively. The wild soybean contributed to the tolerance allele in the progenies. Our results suggest that QTL for alkaline salt tolerance is different from the QTL for NaCl salt tolerance found previously in this wild soybean genotype. The DNA markers closely associated with the QTLs might be useful for marker-assisted selection to pyramid tolerance genes in soybean for both alkaline and saline stresses.     

Mapping quantitative trait loci associated with spot blotch and net blotch resistance in a doubled-haploid barley population

Spot blotch and net blotch are important foliar barley (Hordeum vulgare L.) diseases in Canada and elsewhere. These diseases result in significant yield reduction and, more importantly, loss of grain quality, downgrading barley from malt to feed. Combining resistance to these diseases is a breeding priority but is a significant challenge using conventional breeding methodology. In the present investigation, an evaluation of the inheritance of resistance to spot and net blotch was conducted in a doubled-haploid barley population from the cross CDC Bold (susceptible)?×?TR251 (resistant). The population was screened at the seedling stage in the Phytotron and at the adult-plant stage in the field for several years. Chi-squared analysis indicated one- to four-gene segregation depending on disease, isolate, plant development stage, location and year. A major seedling and adult-plant resistance quantitative trait locus (QTL), designated QRpt6, was re-confirmed for net-form net blotch resistance, explaining 32?C61% of phenotypic variation in different experiments. Additional QTL for seedling and adult-plant resistance to net blotch were identified. For spot blotch resistance, a major seedling resistance QTL (QRcss1) was detected on chromosome 1H for isolate WRS1909, explaining 79% of the phenotypic variation. A highly significant QTL on 3H (QRcs3) was identified for seedling resistance to isolate WRS1908 and adult-plant resistance at Brandon, MB, Canada in 2008. The identification of QTL at only one location or from 1?year suggests spot blotch resistance is complex and highly influenced by the environment. Efforts are being made to combine spot and net blotch resistance in elite barley lines using molecular marker-assisted selection.     

Association mapping of salt tolerance in barley (Hordeum vulgare L.)

A spring barley collection of 192 genotypes from a wide geographical range was used to identify quantitative trait loci (QTLs) for salt tolerance traits by means of an association mapping approach using a thousand SNP marker set. Linkage disequilibrium (LD) decay was found with marker distances spanning 2–8 cM depending on the methods used to account for population structure and genetic relatedness between genotypes. The association panel showed large variation for traits that were highly heritable under salt stress, including biomass production, chlorophyll content, plant height, tiller number, leaf senescence and shoot Na⁺, shoot Cl^? and shoot, root Na⁺/K⁺ contents. The significant correlations between these traits and salt tolerance (defined as the biomass produced under salt stress relative to the biomass produced under control conditions) indicate that these traits contribute to (components of) salt tolerance. Association mapping was performed using several methods to account for population structure and minimize false-positive associations. This resulted in the identification of a number of genomic regions that strongly influenced salt tolerance and ion homeostasis, with a major QTL controlling salt tolerance on chromosome 6H, and a strong QTL for ion contents on chromosome 4H.     

A major QTL conditioning salt tolerance in S-100 soybean and descendent cultivars

Deployment of salt tolerant cultivars is an effective approach to minimize yield loss in a saline soil. In soybean, Glycine max (L.) Merr., substantial genetic variation exists for salt response. However, breeding for salt tolerance is hampered because no economically viable screening method has been developed for practical breeding. To facilitate the development of an effective screening method for salt tolerance in soybean, the present study was conducted to determine the heritability of salt tolerance and to identify associated quantitative trait loci (QTL). F_2:5 lines from the cross of S-100 (salt tolerant) × Tokyo (salt sensitive) were evaluated in a saline field in Hyde County, N.C., USA, in 1999 and in a greenhouse located in Raleigh, N.C., USA, in 2001. S-100 and Tokyo are ancestors of popular soybean cultivars released for the southern USA. The visual salt tolerance ratings of the F_2:5 lines ranged from 0 (complete death) to 5 (normal healthy appearance). The entry-mean heritability for salt tolerance was 0.85, 0.48, and 0.57 in the field (four replications), greenhouse (two replications), and combined environments, respectively. The genotypic correlation between field and greenhouse ratings was 0.55, indicating reasonably good agreement between the two screening environments. To identify QTL associated with salt tolerance, each line was characterized with RFLP markers and an initial QTL single-factor analysis was completed. These results were used to identify genomic regions associated with the trait and to saturate the selected genomic regions with SSR markers to improve mapping precision. Subsequently, a major QTL for salt tolerance was discovered near the Sat_091 SSR marker on linkage group (LG) N, accounting for 41, 60, and 79% of the total genetic variation for salt tolerance in the field, greenhouse, and combined environments, respectively. The QTL allele associated with tolerance was derived from S-100. Pedigree tracking was used to examine the association between the salt tolerance QTL and flanking SSR marker alleles in U.S. cultivars descended from S-100 or Tokyo through 60 years of breeding. The presence of alleles from S-100 at the Sat_091 and Satt237 marker loci was always associated with salt tolerance in descendants. Alleles from Tokyo for these same markers were generally associated with salt sensitivity in descendent cultivars. The strong relationship between the SSR marker alleles and salt tolerance suggests that these markers could be used for marker-assisted selection in commercial breeding.An erratum to this article can be found at