Quantitative trait locus mapping in natural populations: progress, caveats and future directions

Over the last 15 years quantitative trait locus (QTL) mapping has become a popular method for understanding the genetic basis of continuous variation in a variety of systems. For example, the technique is now an integral tool in medical genetics, livestock production, plant breeding and population genetics of model organisms. Ten years ago, it was suggested that the method could be used to understand continuous variation in natural populations. In this review I: (i) clarify what is meant by natural population in the QTL context, (ii) discuss whether evolutionary biologists have successfully mapped QTL in natural populations, (iii) highlight some of the questions that have been addressed by QTL mapping in natural populations, (iv) describe how QTL mapping can be conducted in unmanipulated natural populations, (v) highlight some of the limitations of QTL mapping and (vi) try to predict some future directions for QTL mapping in natural populations.     

Antennal and behavioural response of codling moth Cydia pomonella to plant volatiles

Identification of host volatile compounds attractive to codling moth Cydia pomonella, a most important insect of apple, will contribute to the development of safe control techniques. Synthetic apple volatiles in two doses were tested for antennal and behavioural activity in codling moth. Female antennae strongly responded to (Z)3‐hexenol, (Z)3‐hexenyl benzoate, (Z)3‐hexenyl hexanoate, (±)‐linalool and E,E‐α‐farnesene. Two other compounds eliciting a strong antennal response were the pear ester, ethyl (E,Z)‐2,4‐decadienoate, and its corresponding aldehyde, E,E‐2,4‐decadienal, which is a component of the larval defence secretion of the European apple sawfly. Attraction of codling moth to compounds eliciting a strong antennal response was tested in a wind tunnel. Male moths were best attracted to a blend of (E,E)‐α‐farnesene, (E)‐beta‐farnesene and ethyl (E,Z)‐2,4‐decadienoate. The aldehyde E,E‐2,4‐decadienal had an antagonistic effect when added to the above mixture.     

Enzymatic diagnosis of resistance to deltamethrin in diapausing larvae of the codling moth,Cydia pomonella (L.)

The resistance to deltamethrin was evaluated in diapausing larvae of 14 field populations of the codling moth (Cydia pomonella L.) From the main French orchard areas using biological assays. Resistance to deltamethrin was compared to mixed-function-oxidase (mfo) activity measured at the individual level through ethoxycoumarin-O-deethylase (ECOD) activity using a fluorescence microplate reader. The larvae were collected in corrugated paper band traps in the autumn of 1995. Analysis was previously performed on two laboratory strains, one susceptible and one resistant to deltamethrin, in order to characterize the changes in resistance during diapause development. Resistance to deltamethrin as well as the ECOD activity were stable during the diapause, and ECOD activity was always significantly lower in the susceptible strain than in the resistant one. The ECOD activity was significantly correlated to the frequency of resistant moths in the field populations. This strongly suggested the involvement of the mfo system in the resistance to deltamethrin in these populations. The intra-strain variabilities in ECOD activity of both laboratory and field resistant insects indicated that other resistance mechanisms might also be involved. Further investigations on these mechanisms are needed in order to develop complete diagnostic methods and to define suitable control strategies against each resistant population. Arch. Insect Biochem. Physiol. 39:55–64, 1998. © 1998 Wiley-Liss, Inc.     

Comparative analysis of peach and pear fruit volatiles attractive to the oriental fruit moth,Cydia molesta

Cydia molesta is an important pest of peach and pear fruits late in growing season. We identified and quantified volatiles from immature and mature fruits of peach and pear using gas chromatography-mass spectrometry. Antennally, active compounds were identified by gas chromatography-electroantennogram detection and were further tested in the field. Consistent electroantennographic activity was obtained for nine compounds from headspace collections of the mature fruits of two peach and two pear varieties. Esters were the major components, but qualitative and quantitative differences were found among four odor profiles. Blends mimicking pear fruit volatiles were more attractive to both sexes than blends mimicking peach fruit volatiles in both orchards. Our finding indicated that mixtures mimicking peach and pear fruit volatiles attracted both females and males of C. molesta, and these host volatiles may also be involved in the host switch behavior from peach to pear in mid-late season.     

Quantitative trait loci for resistance to infection in sheep using a live Salmonella Abortusovis vaccine

Quantitative trait loci (QTL) mapping for susceptibility to a Salmonella Abortusovis vaccinal strain was performed using an experimental design involving 30 Romane sheep sire families (1216 progenies). Nine QTL corresponding to bacterial load, weight variations and antibody response criteria were mapped on eight chromosomes, including the major histocompatibility complex area on chromosome 20. Surprisingly, none was found to be significant in the SLC11A1 region (formerly NRAMP1) that has been shown to influence Salmonella susceptibility in other species.     

Mapping of quantitative trait loci for clinical–chemical traits in swine

Clinical–chemical traits are diagnostic parameters essential for characterization of health and disease in veterinary practice. The traits show significant variability and are under genetic control, but little is known about the fundamental genetic architecture of this variability, especially in swine. We have identified QTL for alkaline phosphatase (ALP), lactate (LAC), bilirubin (BIL), creatinine (CRE) and ionized sodium (Na⁺), potassium (K⁺) and calcium (Ca⁺⁺) from the serum of 139 F₂ pigs from a Meishan/Pietrain family before and after challenge with Sarcocystis miescheriana , a protozoan parasite of muscle. After infection, the pigs passed through three stages representing acute disease, subclinical disease and chronic disease. Forty-two QTL influencing clinical–chemical traits during these different stages were identified on 15 chromosomes. Eleven of the QTL were significant on a genome-wide level; 31 QTL were chromosome-wide significant. QTL showed specific health/disease patterns with respect to the baseline values of the traits as well as the values obtained through the different stages of disease. QTL influencing different traits at different times were found primarily on chromosomes 1, 3, 7 and 14. The most prominent QTL for the investigated clinical–chemical traits mapped to SSC3 and 7. Baseline traits of ALP, LAC, BIL, Ca⁺⁺ and K⁺ were influenced by QTL regions on SSC3, 6, 7, 8 and 13. Single QTL explained up to 21.7% of F₂ phenotypic variance. Our analysis confirms that variation of clinical–chemical traits is associated with multiple chromosomal regions.     

分子模拟技术及其在苹果蠹蛾代谢杀虫剂分子机制研究中的应用进展

苹果蠹蛾是世界性重要的果树害虫,也是我国一类进境检疫性有害生物,严重威胁着我国黄土高原和环渤海湾优势苹果产区的果业生产。化学防治是当前苹果蠹蛾防治最经济有效的措施,然而频繁使用化学杀虫剂引发的抗药性问题也在世界范围内相继报道。代谢抗性是苹果蠹蛾抗性中重要的机制,苹果蠹蛾解毒酶代谢杀虫剂的分子机制是当前代谢抗性研究的重点方向。基于分子模拟的方法在相关研究中扮演着越来越重要的角色,本文综述了分子模拟涉及的主要方法及其在苹果蠹蛾代谢杀虫剂分子机制研究中的应用,并展望未来可能的研究方向。     

Quantitative trait loci mapping in dairy cattle: review and meta-analysis

From an extensive review of public domain information on dairy cattle quantitative trait loci (QTL), we have prepared a draft online QTL map for dairy production traits. Most publications (45 out of 55 reviewed) reported QTL for the major milk production traits (milk, fat and protein yield, and fat and protein concentration (%)) and somatic cell score. Relatively few QTL studies have been reported for more complex traits such as mastitis, fertility and health. The collated QTL map shows some chromosomal regions with a high density of QTL, as well as a substantial number of QTL at single chromosomal locations. To extract the most information from these published records, a meta-analysis was conducted to obtain consensus on QTL location and allelic substitution effect of these QTL. This required modification and development of statistical methodologies. The meta-analysis indicated a number of consensus regions, the most striking being two distinct regions affecting milk yield on chromosome 6 at 49 cM and 87 cM explaining 4.2 and 3.6 percent of the genetic variance of milk yield, respectively. The first of these regions (near marker BM143) affects five separate milk production traits (protein yield, protein percent, fat yield, fat percent, as well as milk yield).     

Control of diapausing codling moth,Cydia pomonella (Lepidoptera: Tortricidae) in wooden fruit bins,using entomopathogenic nematodes (Heterorhabditidae and Steinernematidae)

Stacked wooden fruit bins are frequent overwintering sites for overwintering diapausing codling moth larvae. Control strategies against the codling moth (Cydia pomonella) (Lepidoptera: Tortricidae) in South Africa have been hampered by the reinfestation of orchards from nearby stacked infested fruit bins and by the movement of infested bins between orchards. Worldwide, wooden fruit bins are systematically being replaced with plastic bins, however in South Africa this will not be accomplished in the near future. The objective of this study was to evaluate the potential of two recycled commercially available entomopathogenic nematode (EPN) species, Heterorhabditis bacteriophora and Steinernema feltiae, as well as of a local species, Steinernema yirgalemense, to disinfest miniature wooden fruit bins under controlled conditions in the laboratory. After dipping miniature bins loaded with codling moth larvae in a suspension of 25?IJs/mL of each of the three EPN species, under optimum conditions of temperature and humidity, the highest percentage of control was obtained using S. feltiae (75%). The addition of adjuvants significantly increased S. feltiae infectivity to >95%, whereas it did not result in a significant increase in H. bacteriophora or S. yirgalemense infectivity.     

Thermal conditioning of fifth-instar Cydia pomonella (Lepidoptera: Tortricidae) affects HSP70 accumulation and insect mortality

Abstract.  Levels of HSP70 protein of fifth-instar codling moth [ Cydia pomonella (L.) (Lepidoptera: Tortricidae)] are determined after conditioning at 35 °C for different times and also after recovery at 22 °C. Protein samples from larvae conditioned for different times are separated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis electrophoresis. Sub-lethal thermal conditioning at 35 °C for 40 min, 2, 6 and 18 h induces new protein bands in the extracts from treated codling moth larvae. Immunodetection with an antibody to a heat-inducible HSP70 indicates a stronger reaction after 35 °C for 2, 6 and 18 h than after 35 °C for 40 min or control and, during the recovery period at 22 °C, the level of heat shock protein decreases. Conditioning of fifth-instar codling moths at 35 °C also induces thermotolerance in the insects and necessitates longer times at a lethal temperature to ensure mortality. Thermotolerance is correlated with the accumulation of heat inducible HSP70 protein.     

Genetic mapping of three quantitative trait loci for soybean aphid resistance in PI 567324

Host-plant resistance is an effective method for controlling soybean aphid (Aphis glycines Matsumura), the most damaging insect pest of soybean (Glycine max (L.) Merr.) in North America. Recently, resistant soybean lines have been discovered and at least four aphid resistance genes (Rag1, Rag2, Rag3 and rag4) have been mapped on different soybean chromosomes. However, the evolution of new soybean aphid biotypes capable of defeating host-plant resistance conferred by most single genes demonstrates the need for finding germplasm with multigenic resistance to the aphid. This study was conducted to map quantitative trait loci (QTL) for aphid resistance in PI 567324. We identified two major QTL (QTL_13_1 and QTL_13_2) for aphid resistance on soybean chromosome 13 using 184 recombinant inbred lines from a ‘Wyandot'' × PI 567324 cross. QTL_13_1 was located close to the previously reported Rag2 gene locus, and QTL_13_2 was close to the rag4 locus. A minor QTL (QTL_6_1) was also detected on chromosome 6, where no gene for soybean aphid resistance has been reported so far. These results indicate that PI 567324 possesses oligogenic resistance to the soybean aphid. The molecular markers closely linked to the QTL reported here will be useful for development of cultivars with oligogenic resistance that are expected to provide broader and more durable resistance against soybean aphids compared with cultivars with monogenic resistance.     

Confirmation of two quantitative trait loci regions for nematode resistance in commercial British terminal sire breeds

Sheep internal parasites (nematodes) remain a major health challenge and are costly for pasture-based production systems. Most current breeding programmes for nematode resistance are based on indicator traits such as faecal egg counts (FEC), which are costly and laborious to collect. Hence, genetic markers for resistance would be advantageous. However, although some quantitative trait loci (QTL) have been identified, these QTL are often not consistent across breeds and few breeding strategies for nematode resistance in sheep are currently using molecular information. In this study, QTL for nematode resistance on ovine chromosomes (OAR) 3 and 14, previously identified in the Blackface breed, were explored using commercial Suffolk (n = 336) and Texel lambs (n = 879) sampled from terminal sire breeder flocks in the United Kingdom. FEC were used as the indicator trait for nematode resistance, and these were counted separately for Nematodirus and Strongyles genera. Microsatellite markers were used to map the QTL and the data were analysed using interval mapping regression techniques and variance component analysis. QTL for Nematodirus and Strongyles FEC were found to be segregating on OAR3 at 5% chromosome region-wide significance threshold in both Suffolk and Texel sheep, and Nematodirus FEC QTL were segregating on OAR14 in both breeds. In addition, QTL for growth traits were also found to be segregating at 5% chromosome region-wide on OAR3 and OAR14. The confirmation that FEC QTL segregate in the same position in three widely used breeds widens their potential applicability to purebred Blackface, Suffolk and Texel sheep, with benefits likely to be observed in their commercial crossbred progeny.     

Quantitative trait locus analysis of lateral branch– related traits in cucumber (Cucumis sativus L.) using recombinant inbred lines

A group of 224 recombinant inbred lines (RILs) was derived from a narrow cross between 2 cucumber (Cucumis sativus L.) lines, namely, S94 (Northern China type with weak lateral branch growth potential and early lateral branch sprouting time) and S06 (Northern European type with strong lateral branch growth potential and late lateral branch sprouting time). These lines were then used for investigating lateral branch-related traits. A total of 36 quantitative trait loci (QTLs) were detected for the following 4 lateral branch-related traits: lateral branch average length (LBAL), lateral branch total length (LBTL), lateral branch number (LBN), and first lateral branch node (FLBN). Further, each QTL explained 3.1% (lbtl2.1, spring) to 32.3% (lbn2.3, spring) of the observed phenotypic variance. Eleven QTLs (lbal1.1, lbtl1.1, lbn1.2, flbn1.2, etc.) for different traits were found to be clustered on the e23m18d-ME23EM6c section (7.4 cM) of linkage group (LG) 1; further, 15 QTLs (lbal2.1, lbtl2.1, lbn2.1, flbn2.1, etc.) were found to be clustered on the S94A1-ME4SA4a section (13.9 cM) of LG2. Twenty-one QTLs explained more than 10% of the phenotypic variance. Moreover, lbtl1.3 (autumn, 26.2%, logarithm of odds (LOD) = 17.4; spring, 26.9%, LOD = 17.9) had stable position and contribution in both seasons. Several se-quence-anchor markers (CMBR40, F, CS30, S94A1, CSWTA11B, etc.) were closely linked with some QTLs for LBAL, LBTL, LBN, and FLBN, which can be used for the marker-assisted selection to improve the plant architecture in cucumber breeding.     

Up-regulation of two cDNA clones encoding metallothionein-like proteins in apple fruit during cool storage

We are investigating the molecular basis of low temperature responses in apples, by identifying and characterising fruit genes which show altered expression in response to cool-storage, Two independent cold-regulated clones (pAMTI and pAMT2) were isolated from a cDNA library derived from cool-stored apple ( Malus domestics Borkh. cv. Granny Smith) fruit. These clones share only 27% amino acid identity with each other, but both show high similarity to plant metallothionein (MT)-like proteins. The polypeptide encoded by pAMTI shares similarity with type 2 MT-like sequences, while that encoded by pAMT2 is similar to others which share a different distribution of cysteine residues. We suggest, these form a 'type 3' group of MT-like clones. Genomic Southern analysis confirmed that there is a family of MT-like genes in apple. There are differing patterns of pAMTI and pAMT2 expression during apple fruit development, amt 1 RNA was abundant in flowers and during the early stages of development, and decreased as the fruit approached maturity, while amt 2 RNA was barely detectable in flowers and young fruit and accumulated with fruit development. In ripe fruit. amt 1. expression was up-regulated, while amt 2 expression was down-regulated. In leaves, both genes showed increased expression with leaf age. In Granny Smith, Cox's Orange Pippin and Braeburn apple cultivars. both genes were up-regulated in cool-stored fruit. In Granny Smith contical tissue, amt RNA levels were elevated within the first 45 min at both 0.5°C and 4°C, but not at 12.5°C. The different patterns of amt 1 and amt 2 expression during fruit development and in different tissues suggest that the respective genes have distinct controlling elements and may be functionally different. The in vivo roles of the encoded polypeptides, particularly in relation to chilling tolerance or acclimation, are as yet unknown.     

寄主植物信息化合物对苹果蠹蛾行为的影响及其在防控中的应用

苹果蠹蛾（Cydia pomonella)是仁果类水果的重要世界性害虫,也是我国的重要检疫性对象,在我国的发生、危害及潜在扩张的趋势十分严峻.有关寄主植物气味对苹果蠹蛾特异性引诱方面的研究受到了广泛的关注.本文综述了苹果蠹蛾和植物源气味之间的互作关系,主要包括寄主植物气味影响苹果蠹蛾成虫寄主定位、求偶交配和产卵等行为,幼虫取食对寄主植物气味释放以及寄主植物气味对性信息素的影响;同时还介绍了主要植物源化合物梨酯的研究和田间应用概况,以期为我国苹果蠹蛾的防控研究和应用提供参考.     

Quantitative trait loci mapping of adult-plant resistance to powdery mildew in triticale

Powdery mildew (PM) is a common disease caused by Blumeria graminis, which affects cereals and has recently adapted to triticale. Adult-plant resistance (APR) genes provide durable protection of crops from the disease. Quantitative trait loci corresponding to the APR effects were mapped in an F₂ population of “Lamberto” (susceptible) × “Moderto” (resistant). A genetic map of winter triticale was constructed based on the segregation of 863 DArT, 38 microsatellite and 10 resistance gene analogue markers. Composite interval mapping (CIM) was applied to identify three QTLs for maximum disease severity (MDS) and two for the area under disease progress curve (AUDPC) conferring resistance to the powdery mildew on chromosomes: 6A, 7A, 1B and 4R. The 39% variation in AUDPC was explained by the main QTL localised on chromosome 4R. Genes coding TRIUR3 proteins, serine/threonine protein kinase and cell wall associated kinases were localised in silico within the QTL and alternative DNA markers were proposed for flexible use in laboratories of diversified throughput.     

Analysis of quantitative trait loci underlying the traits related to chlorophyll content of the flag leaf in rice

A population of 117 doubled haploid (DH) lines derived from the cross of Zhaiyeqing 8 (indica)× Jingxi 17 (japonica) was employed to map quantitative trait loci (QTL) underlying four physiological traits related to chlorophyll contents of the flag leaf. There were significantly positive correlations among chlorophyll a, chlorophyll b and chlorophyll a + b content. Chlorophyll a/b ratio was significantly negatively correlated with chlorophyll b content. These four traits were normally distributed with transgressive segregation, suggesting that they were controlled by multiple minor genes. A total of 11 QTLs were detected for the four traits and they lay on six chromosomes. Each of them explained 9.2%–19.6% of the phenotypic variations, respectively. Of these, two QTLs controlling chlorophyll a content were mapped on chromosomes 2 and 5; four QTLs underlying chlorophyll b content were mapped on chromosomes 2, 3, 5 and 9; three QTLs underlying chlorophyll a + b amount were mapped on chromosomes 3, 5 and 9; two QTLs underlying chlorophyll a/b ratio were mapped on chromosomes 6 and 11. The intrinsic relationship among the four traits and the practical implication in rice breeding are discussed. __________ Translated from Journal of Wuhan University (Science Edition), 2006, 52(6): 751–756 [译自: 武汉大学学报(理学版)]     

Analysis of quantitative trait loci underlying the traits related to chlorophyll content of the flag leaf in rice

A population of 117 doubled haploid (DH) lines derived from the cross of Zhaiyeqing 8 (indica) x Jingxi 17 (japonica) was employed to map quantitative trait loci (QTL) underlying four physiological traits related to chlorophyll contents of the flag leaf. There were significantly positive correlations among chlorophyll a, chlorophyll b and chlorophyll a+ b content. Chlorophyll a/b ratio was significantly negatively correlated with chlorophyll b content. These four traits were normally distributed with transgressive segregation, suggesting that they were controlled by multiple minor genes. A total of 11 QTLs were detected for the four traits and they lay on six chromosomes. Each of them explained 9.2%-19.6% of the phenotypic variations, respectively. Of these, two QTLs controlling chlorophyll a content were mapped on chromosomes 2 and 5; four QTLs underlying chlorophyll b content were mapped on chromosomes 2, 3, 5 and 9; three QTLs underlying chlorophyll a+b amount were mapped on chromosomes 3, 5 and 9; two QTLs under-lying chlorophyll a/b ratio were mapped on chromosomes 6 and 1 1. The intrinsic relationship among the four traits and the practical implication in rice breeding are discussed.     

Genetic mapping of quantitative trait loci for resistance to Haemonchus contortus in sheep

This paper presents results from a mapping experiment to detect quantitative trait loci (QTL) for resistance to Haemonchus contortus infestation in merino sheep. The primary trait analysed was faecal worm egg count in response to artificial challenge at 6 months of age. In the first stage of the experiment, whole genome linkage analysis was used for broad-scale mapping. The animal resource used was a designed flock comprising 571 individuals from four half-sib families. The average marker spacing was about 20 cM. For the primary trait, 11 QTL (as chromosomal/family combinations) were significant at the 5% chromosome-wide level, with allelic substitution effects of between 0.19 and 0.38 phenotypic standard deviation units. In general, these QTL did not have a significant effect on faecal worm egg count recorded at 13 months of age. In the second stage of the experiment, three promising regions (located on chromosomes 1, 3 and 4) were fine-mapped. This involved typing more closely spaced markers on individuals from the designed flock as well as an additional 495 individuals selected from a related population with a deeper pedigree. Analysis was performed using a linkage disequilibrium–linkage approach, under additive, dominant and multiple QTL models. Of these, the multiple QTL model resulted in the most refined QTL positions, with resolutions of <10 cM achieved for two regions. Because of the moderate size of effect of the QTL, and the apparent age and/or immune status specificity of the QTL, it is suggested that a panel of QTL will be required for significant genetic gains to be achieved within industry via marker-assisted selection.