Genetic mapping of quantitative trait loci governing longevity of Caenorhabditis elegans in recombinant-inbred progeny of a Bergerac-BO x RC301 interstrain cross

Recombinant-inbred populations, generated from a cross between Caenorhabditis elegans strains Bergerac-BO and RC301, were used to identify quantitative trait loci (QTL) affecting nematode longevity. Genotypes of young controls and longevity-selected worms (the last-surviving 1% from a synchronously aged population) were assessed at dimorphic transposon-specific markers by multiplex polymerase chain reaction. The power of genetic mapping was enhanced, in a novel experimental design, through map expansion by accrual of recombinations over several generations, internally controlled longevity selection from a genetically heterogeneous, homozygous population, and selective genotyping of extremely long-lived worms. Analysis of individual markers indicated seven life-span QTL, situated near markers on chromosomes I (tcbn2), III (stP127), IV (stP13), V (stP6, stP23, and stP128), and X (stP41). These loci were corroborated, and mapped with increased precision, by nonparametric interval mapping-which supported all loci implicated by single-marker analysis. In addition, a life-span QTL on chromosome II (stP100-stP196), was significant only by interval mapping. Congenic lines were constructed for the longevity QTL on chromosomes III and X, by backcrossing the Bergerac-BO QTL allele into an RC301 background with selection for flanking markers. Survival data for these lines demonstrated consistent and significant effects of each QTL on life span.     

Mapping Quantitative Trait Loci Affecting Life History Traits in the Nematode Caenorhabditis Elegans

We have identified chromosomal regions containing quantitative trait loci (QTLs) specifying life history traits in recombinant-inbred strains of the nematode Caenorhabditis elegans. This approach also allows us to examine epistatic interactions between loci and pleiotropic effects on different traits at specific loci. QTLs for mean life span were identified on chromosomes II (near stP101), IV (stP5) and the X (stP61), and QTLs for fertility were identified on II (maP1), III (stP19) and IV (stP51). The QTLs for mean life span accounted for 90% of the genetic component of variance. The loci for mean fertility accounted for 88% of the genetic component of variance. Additional QTLs for temperature-sensitive fertility [II (stP36) and V (stP6)] and internal hatching [IV (stP5)] were also mapped in these crosses. We found evidence for epistatic effects on mean life span between maP1 and bP1 (V), and for epistatic effects on mean fertility between stP36 and stP6, between stP98 (II) and stP192 (V), between maP1 and stP127 (III), between maP1 and stP103 (X), and between stP5 and stP6. Negatively correlated, pleiotropic effects on mean life span and internal hatching were found linked to stP5.     

Quantitative trait loci analysis of leaf and plant longevity in Arabidopsis thaliana

The natural variation in leaf and plant longevity in Arabidopsis thaliana was analysed in a set of 45 ecotypes and 155 recombinant inbred lines derived from a Cape Verde Islands (Cvi) x Landsberg erecta (Ler) cross. Post-bolting longevity was inversely related to time to flowering and rosette leaf number in the set of 45 ecotypes, with Cvi having the longest and Ler the shortest post-bolting longevity. The recombinant inbred line population was tested under low or high soil nutrient levels (LN or HN, respectively). Three quantitative trait loci (QTL), one in chromosome 3 and two in chromosomes 1 and 5, were associated with longevity of the 6th rosette leaf under LN and HN, respectively. Four QTL for post-bolting longevity were found in chromosomes 1, 3, 4, and 5, and two in chromosomes 1 and 5 under LN and HN, respectively. An epistatic interaction affecting post-bolting longevity under LN, but not HN, was detected. Ler and Cvi carry a mix of increasing and decreasing alleles for the QTL affecting longevity of the 6th leaf and post-bolting longevity. Longevity of the 6th rosette leaf was associated with different QTL than post-bolting longevity, and it was affected by different QTL depending on nutrient availability. By contrast, the major QTL affecting post-bolting longevity exerted significant effects irrespective of soil nutrient availability.     

Genome-wide association study for longevity in the Holstein cattle population

Longevity is one of the most important traits determining dairy cow profitability. In the last decades dairy cows suffered a lowering in the age at culling. With the aim to identify the genes involved in longevity, dates of birth, yields, dates of calving during lifespan and culling dates were collected for 946 culled cows which had been genotyped with the Bovine High Density panel. Using the GenABEL package in R, genome-wide association analysis was performed on three potential traits of longevity: (1) ‘days in production,’ (2) ‘days in herd,’ (3) number of calvings over lifespan.’ Five genome-wide significant single nucleotide polymorphisms (SNPs) associated with all three longevity traits were detected. Several consecutive SNPs identified on chromosomes 16 and 30 indicated the presence of two suggestive quantitative trait loci (QTL). The genes comprised in the QTL regions had biological functions related to fertility, reproductive disorders, heat stress and welfare of cows. These findings might contribute to improving breeding strategies to improve longevity.     

QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum)

Interval mapping of quantitative trait loci (QTL) for 16 yield, agronomic and quality traits in potato was performed on a tetraploid full-sib family comprising 227 clones from a cross between processing clone 12601ab1 and table cultivar Stirling. Thirty-eight AFLP primer combinations and six SSRs provided 514 informative markers which formed a molecular marker map comprising 12 linkage groups (LGs) in 12601ab1 (nine with four homologous chromosomes) which were aligned with 12 in Stirling (11 with four homologous chromosomes), with four partial groups remaining in 12601ab1. Two LGs were identified unequivocally as chromosomes IV and V and eight others were tentatively assigned with chromosomes VII and X unidentified. All of the traits scored had moderately high heritabilities with 54–92% of the variation in clone means over 3 years and two replicates being due to genetic differences. A total of 39 QTLs were identified. A QTL for maturity was identified on chromosome V which explained 56% of the phenotypic variance, whereas the other QTLs individually explained between 5.4 and 16.5%. However, six QTLs were detected for after-cooking blackening and four for each of regularity of tuber shape, fry colour both after storage at 4 and 10°C and sprouting. Just two QTLs were found for each of yield, the two ‘overall’ scores, crop emergence, tuber size and common scab and just one QTL was detected for each of dry matter content, keeping quality, growth cracks and internal condition. The implications for practical potato breeding and for practical linkage and QTL analysis in autotetraploids are discussed.     

Genetic mapping of quantitative trait loci affecting body weight, egg character and egg production in F2 intercross chickens

Phenotypic measurements of chicken egg character and production traits are restricted to mature females only. Marker assisted selection of immature chickens using quantitative trait loci (QTL) has the potential to accelerate the genetic improvement of these traits in the chicken population. The QTL for 12 traits (i.e. body weight (BW), six for egg character, three for egg shell colour and two for egg production) of chickens were identified. An F2 population comprising 265 female chickens obtained by crossing White Leghorn and Rhode Island Red breeds and genotyped for 123 microsatellite markers was used for detecting QTL. Ninety-six markers were mapped on 25 autosomal linkage groups, and 13 markers were mapped on one Z chromosomal linkage group. Eight previous unmapped markers were assigned to their respective chromosomes in this study. Significant QTL were detected for BW on chromosomes 4 and 27, egg weight on chromosome 4, the short length of egg on chromosome 4, and redness of egg shell colour (using the L*a*b* colour system) on chromosome 11. A significant QTL on the Z chromosome was linked with age at first egg. Significant QTL could account for 6-19% of the phenotypic variance in the F2 population.     

Genetics of quantitative traits in Arabidopsis thaliana

The genetic control of 22 quantitative traits, including developmental rates and sizes, was examined in generations of Arabidopsis thaliana derived from the cross between the ecotypes, Columbia (Col) and Landsberg erecta (Ler). The data were obtained from three sets of families raised in the same trial: the 16 basic generations, that is, parents, F(1)'s, F(2)'s, backcrosses, recombinant inbred lines (RILs) and a triple test cross (TTC), the latter produced by crossing the RILs to Col, Ler and their F(1). The data were analysed by two approaches. The first (approach A) involved traditional generation mean and variance component analysis and the second (B), based around the RILs and TTC families, involved marker-based QTL analysis.From (A), genetic differences between Col and Ler were detected for all traits with moderate heritabilities. Height at flowering was the only trait to show heterosis. Dominance was partial to complete for all height traits, and there was no overdominance but there was strong evidence for directional dominance. For most other traits, dominance was ambidirectional and incomplete, with average dominance ratios of around 80%. Epistasis, particularly of the duplicate type that opposes dominance, was a common feature of all traits. The presence of epistasis must imply multiple QTL for all traits.The QTL analysis located 38 significant effects in four regions of chromosomes I, II, IV and V, but not III. QTL affecting rosette size and leaf number were identified in all four regions, with days to maturity on chromosomes IV and V. The only QTL for height was located at the expected position of the erecta gene (chromosome II; 50 cM), but the additive and dominance effects of this single QTL did not adequately explain the generation means. The possible involvement of other interacting height QTL is discussed.     

Genetic mapping of quantitative trait loci for meat quality and muscle metabolic traits in cattle

A whole‐genome scan was carried out in New Zealand and Australia to detect quantitative trait loci (QTL) for live animal and carcass composition traits and meat quality attributes in cattle. Backcross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. This paper reports on meat quality traits (tenderness measured as shear force at 4–5 ages on two muscles as well as associated traits of meat colour, pH and cooking loss) and a number of metabolic traits. For meat quality traits, 18 significant QTL (P < 0.05), located in nine linkage groups, were detected on a genome‐wise basis, in combined‐sire (seven QTL) or within‐sire analyses (11 QTL). For metabolic traits, 11 significant QTL (P < 0.05), located in eight linkage groups, were detected on a genome‐wise basis, in combined‐sire (five QTL) or within‐sire analyses (six QTL). BTA2 and BTA3 had QTL for both metabolic traits and meat quality traits. Six significant QTL for meat quality and metabolic traits were found at the proximal end of chromosome 2. BTA2 and BTA29 were the most common chromosomes harbouring QTL for meat quality traits; QTL for improved tenderness were associated with Limousin‐derived and Jersey‐derived alleles on these two chromosomes, respectively.     

QTL for tuber morphology traits in diploid potato

A diploid, potato mapping population consisting of 149 individuals was assessed in three consecutive years for important agronomic and quality traits: tuber shape, regularity of tuber shape, eye depth, mean tuber weight, and tuber flesh color. Analysis of variance showed that the genotype had the largest influence on the phenotypic scores but effect of the genotype × year interactions was also strong. Using this data and an existing genetic map, a quantitative trait loci (QTL) analysis was conducted. From four to seven QTL were detected for each trait except tuber flesh color, which was determined by a major QTL on chromosome III explaining 76.8% of the trait variance. Additionally, a minor QTL for flesh color was localized on chromosome II. For the other traits, significant QTL were detected: for tuber shape on chromosome X, for regularity of tuber shape on chromosome III, for eye depth on chromosome IV, and for tuber weight on chromosome I. Some detected QTL confirmed previous studies, but new ones were also identified.     

Quantitative trait loci for porcine baseline erythroid traits at three growth ages in a White Duroc × Erhualian F<Subscript>2</Subscript> resource population

Baseline erythroid indices are increasingly involved as risk factors for common complex diseases in humans. However, little is known about the genetic architecture of baseline erythroid traits in pigs. In this study, hematocrit (Hct), hemoglobin (Hgb), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell (RBC), and red cell distribution width (RDW) were measured in 1420 (day 18), 1410 (day 46), and 1033 (day 240) F(2) pigs from a White Duroc x Erhualian intercross resource population. The entire resource population was genotyped for 183 microsatellite loci across the pig genome, and the quantitative trait loci (QTL) analysis was performed for all erythroid-related traits measured with QTL Express based on a least-squares method. A total of 101 QTL, including 46 genome-wide significant QTL and 55 chromosome-wide significant QTL, regulating erythroid traits were found on all pig chromosomes (SSC) except for SSC15 and SSC18. The genome-wide significant QTL were mainly localized on SSC1, 7, 8, 10, and X. These results confirmed most of QTL previously identified in the swine. More importantly, this study detected age-specific QTL for baseline erythroid traits in pigs for the first time. Notably, the QTL for MCV and MCH on day 18 on SSC8 with small intervals of 3 and 4 cM, respectively, provided a good starting point for identifying causal genes underlying MCV and MCH in the future.     

Identification of trait-improving quantitative trait loci alleles from a wild rice relative,Oryza rufipogon.

Wild species are valued as a unique source of genetic variation, but they have rarely been used for the genetic improvement of quantitative traits. To identify trait-improving quantitative trait loci (QTL) alleles from exotic species, an accession of Oryza rufipogon, a relative of cultivated rice, was chosen on the basis of a genetic diversity study. An interspecific BC2 testcross population (V20A/O. rufipogon//V20B///V20B////Ce64) consisting of 300 families was evaluated for 12 agronomically important quantitative traits. The O. rufipogon accession was phenotypically inferior for all 12 traits. However, transgressive segregants that outperformed the original elite hybrid variety, V20A/Ce64, were observed for all traits examined. A set of 122 RFLP and microsatellite markers was used to identify QTL. A total of 68 significant QTL were identified, and of these, 35 (51%) had beneficial alleles derived from the phenotypically inferior O. rufipogon parent. Nineteen (54%) of these beneficial QTL alleles were free of deleterious effects on other characters. O. rufipogon alleles at two QTL on chromosomes 1 and 2 were associated with an 18 and 17% increase in grain yield per plant, respectively, without delaying maturity or increasing plant height. This discovery suggests that the innovative use of molecular maps and markers can alter the way geneticists utilize wild and exotic germplasm.     

Molecular mapping in tropical maize (Zea mays L.) using microsatellite markers. 2. Quantitative trait loci (QTL) for grain yield, plant height, ear height and grain moisture

A previous genetic map containing 117 microsatellite loci and 400 F(2) plants was used for quantitative trait loci (QTL) mapping in tropical maize. QTL were characterized in a population of 400 F(2:3) lines, derived from selfing the F(2) plants, and were evaluated with two replications in five environments. QTL determinations were made from the mean of these five environments. Grain yield (GY), plant height (PH), ear height (EH) and grain moisture (GM) were measured. Variance components for genotypes (G), environments (E) and GxE interaction were highly significant for all traits. Heritability was 0.69 for GY, 0.66 for PH, 0.67 for EH and 0.23 for GM. Using composite interval mapping (CIM), a total of 13 distinct QTLs were identified: four for GY, four for PH and five for EH. No QTL was detected for GM. The QTL explained 32.73 % of the phenotypic variance of GY, 24.76 % of PH and 20.91 % of EH. The 13 QTLs displayed mostly partial dominance or overdominance gene action and mapped to chromosomes 1, 2, 7, 8 and 9. Most QTL alleles conferring high values for the traits came from line L-14-4B. Mapping analysis identified genomic regions associated with two or more traits in a manner that was consistent with correlation among traits, supporting either pleiotropy or tight linkage among QTL. The low number of QTLs found, can be due to the great variation that exists among tropical environments.     

QTL analysis of falling number and seed longevity in wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Pre-harvest sprouting (PHS) and seed longevity (SL) are complex biological processes of major importance for agricultural production. In the present study, a recombinant inbred line (RIL) population derived from a cross between the German winter wheat (Triticum aestivum L.) cultivars History and Rubens was used to identify genetic factors controlling these two physiological seed traits. A falling number (FN) test was employed to evaluate PHS, while SL was measured using a germination test (and the speed of germination) after controlled deterioration. FN of the population was assessed in four environments; SL traits were measured in one environment. Four major quantitative trait loci (QTL) for FN were detected on chromosomes 4D, 5A, 5D, and 7B, whereas for SL traits, a major QTL was found on chromosome 1A. The FN QTL on chromosome 4D that coincided with the position of the dwarfing gene Rht-D1b only had effects in environments that were free of PHS. The remaining three QTL for FN were mostly pronounced under conditions conducive to PHS. The QTL on the long arm of chromosome 7B corresponded to the major gene locus controlling late maturity α-amylase (LMA) in wheat. The severity of the LMA phenotype became truly apparent under sprouting conditions. The position on the long arm of chromosome 1A of the QTL for SL points to a new QTL for this important regenerative seed trait.     

Genomewide analysis of epistatic effects for quantitative traits in barley

The doubled-haploid (DH) barley population (Harrington x TR306) developed by the North American Barley Genome Mapping Project (NABGMP) for QTL mapping consisted of 145 lines and 127 markers covering a total genome length of 1270 cM. These DH lines were evaluated in approximately 25 environments for seven quantitative traits: heading, height, kernel weight, lodging, maturity, test weight, and yield. We applied an empirical Bayes method that simultaneously estimates 127 main effects for all markers and 127(127-1)/2=8001 interaction effects for all marker pairs in a single model. We found that the largest main-effect QTL (single marker) and the largest epistatic effect (single pair of markers) explained approximately 18 and 2.6% of the phenotypic variance, respectively. On average, the sum of all significant main effects and the sum of all significant epistatic effects contributed 35 and 6% of the total phenotypic variance, respectively. Epistasis seems to be negligible for all the seven traits. We also found that whether two loci interact does not depend on whether or not the loci have individual main effects. This invalidates the common practice of epistatic analysis in which epistatic effects are estimated only for pairs of loci of which both have main effects.     

QTL analysis of ergot resistance in sorghum

Sorghum ergot, caused predominantly by Claviceps africana Frederickson, Mantle, de Milliano, is a significant threat to the sorghum industry worldwide. The objectives of this study were firstly, to identify molecular markers linked to ergot resistance and to two pollen traits, pollen quantity (PQ) and pollen viability (PV), and secondly, to assess the relationship between the two pollen traits and ergot resistance in sorghum. A genetic linkage map of sorghum RIL population R931945-2-2 x IS 8525 (resistance source) was constructed using 303 markers including 36 SSR, 117 AFLPtrade mark, 148 DArTtrade mark and two morphological trait loci. Composite interval mapping identified nine, five, and four QTL linked to molecular markers for percentage ergot infection (PCERGOT), PQ and PV, respectively, at a LOD >2.0. Co-location/linkage of QTL were identified on four chromosomes while other QTL for the three traits mapped independently, indicating that both pollen and non pollen-based mechanisms of ergot resistance were operating in this sorghum population. Of the nine QTL identified for PCERGOT, five were identified using the overall data set while four were specific to the group data sets defined by temperature and humidity. QTL identified on SBI-02 and SBI-06 were further validated in additional populations. This is the first report of QTL associated with ergot resistance in sorghum. The markers reported herein could be used for marker-assisted selection for this important disease of sorghum.     

大豆油份含量QTL的定位

以大豆杂交组合皖82-178×通山薄皮黄豆甲衍生的重组自交系群体(RIL)为材料, 以该群体所构建的遗传连锁图谱为基础, 以2004和2005年油份含量为指标, 利用软件Cartgrapher(V. 2.0)采用复合区间作图法进行了QTL分析, 结果表明, 利用两年资料对油份含量QTL的定位结果基本一致。两年资料所检测到的QTL均位于wt-11连锁群的satt331附近, 分别可以解释13.95%和15.01%遗传变异。此外, 利用软件QTL Mapper 1.6, 采用复合区间作图法直接对两年的油份含量进行QTL联合分析, 结果表明, 控制油份的QTL也位于wt-11连锁群的satt331附近。     

Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc × Chinese Erhualian resource population

Carcass and meat quality traits are economically important in pigs. In this study, 17 carcass composition traits and 23 meat quality traits were recorded in 1028 F₂ animals from a White Duroc × Erhualian resource population. All pigs in this experimental population were genotyped for 194 informative markers covering the entire porcine genome. Seventy-seven genome-wide significant quantitative trait loci (QTL) for carcass traits and 68 for meat quality were mapped to 34 genomic regions. These results not only confirmed many previously reported QTL but also revealed novel regions associated with the measured traits. For carcass traits, the most prominent QTL was identified for carcass length and head weight at 57 cM on SSC7, which explained up to 50% of the phenotypic variance and had a 95% confidence interval of only 3 cM. Moreover, QTL for kidney and spleen weight and lengths of cervical vertebrae were reported for the first time in pigs. For meat quality traits, two significant QTL on SSC5 and X were identified for both intramuscular fat content and marbling score in the longissimus muscle, while three significant QTL on SSC1 and SSC9 were found exclusively for IMF. Both LM and the semimembranous muscle showed common QTL for colour score on SSC4, 5, 7, 8, 13 and X and discordant QTL on other chromosomes. White Duroc alleles at a majority of QTL detected were favourable for carcass composition, while favourable QTL alleles for meat quality originated from both White Duroc and Erhualian.     

Quantitative trait loci for fertility traits in Finnish Ayrshire cattle

A whole genome scan was carried out to detect quantitative trait loci (QTL) for fertility traits in Finnish Ayrshire cattle. The mapping population consisted of 12 bulls and 493 sons. Estimated breeding values for days open, fertility treatments, maternal calf mortality and paternal non-return rate were used as phenotypic data. In a granddaughter design, 171 markers were typed on all 29 bovine autosomes. Associations between markers and traits were analysed by multiple marker regression. Multi-trait analyses were carried out with a variance component based approach for the chromosomes and trait combinations, which were observed significant in the regression method. Twenty-two chromosome-wise significant QTL were detected. Several of the detected QTL areas were overlapping with milk production QTL previously identified in the same population. Multi-trait QTL analyses were carried out to test if these effects were due to a pleiotropic QTL affecting fertility and milk yield traits or to linked QTL causing the effects. This distinction could only be made with confidence on BTA1 where a QTL affecting milk yield is linked to a pleiotropic QTL affecting days open and fertility treatments.     

A composite method for mapping quantitative trait loci without interference of female achiasmatic and gender effects in silkworm,Bombyx mori

The silkworm, Bombyx mori, is an economically important insect that was domesticated more than 5000 years ago. Its major economic traits focused on by breeders are quantitative traits, and an accurate and efficient QTL mapping method is necessary to explore their genetic architecture. However, current widely used QTL mapping models are not well suited for silkworm because they ignore female achiasmate and gender effects. In this study, we propose a composite method combining rational population selection and special mapping methods to map QTL in silkworm. By determining QTL for cocoon shell weight (CSW), we demonstrated the effectiveness of this method. In the CSW mapping process, only 56 markers were used and five loci or chromosomes were detected, more than in previous studies. Additionally, loci on chromosomes 1 and 11 dominated and accounted for 35.10% and 15.03% of the phenotypic variance respectively. Unlike previous studies, epistasis was detected between loci on chromosomes 11 and 22. These mapping results demonstrate the power and convenience of this method for QTL mapping in silkworm, and this method may inspire the development of similar approaches for other species with special genetic characteristics.     

Genetic mapping of quantitative trait loci affecting susceptibility in chicken to develop pulmonary hypertension syndrome

Pulmonary hypertension syndrome (PHS), also referred to as ascites syndrome, is a growth-related disorder of chickens frequently observed in fast-growing broilers with insufficient pulmonary vascular capacity at low temperature and/or at high altitude. A cross between two genetically different broiler dam lines that originated from the White Plymouth Rock breed was used to produce a three-generation population. This population was used for the detection and localization of quantitative trait loci (QTL) affecting PHS-related traits. Ten full-sib families consisting of 456 G2 birds were typed with 420 microsatellite markers covering 24 autosomal chromosomes. Phenotypic observations were collected on 4202 G3 birds and a full-sib across family regression interval mapping approach was used to identify QTL. There was statistical evidence for QTL on chicken chromosome 2 (GGA2), GGA4 and GGA6. Suggestive QTL were found on chromosomes 5, 8, 10, 27 and 28. The most significant QTL were located on GGA2 for right and total ventricular weight as percentage of body weight (%RV and %TV respectively). A related trait, the ratio of right ventricular weight as percentage to total ventricular weight (RATIO), reached the suggestive threshold on this chromosome. All three QTL effects identified on GGA2 had their maximum test statistic in the region flanked by markers MCW0185 and MCW0245 (335-421 cM).