Moving from QTL experimental results to the utilization of QTL in breeding programmes

Results from quantitative trait loci studies cannot be readily implemented into breeding schemes through marker assisted selection because of uncertainty about whether the quantitative trait loci identified are real and whether the identified quantitative trait loci are segregating in the breeding population. The present paper outlines and discusses strategies to reduce uncertainty in the results from quantitative trait loci studies. One strategy to confirm results from quantitative trait loci studies is to combine P -values from many quantitative trait loci experiments, while another is to establish a confirmation study. The power of a confirmation study must be high to ensure that the postulated quantitative trait loci can be verified. In the calculation of the experimental power, there are many issues that have to be addressed: size of the quantitative trait loci to be detected, significance level required, experimental design and expected heterozygosity for the design. To ensure marker assisted selection can be quickly implemented once quantitative trait loci are confirmed, DNA samples should be retained from daughters, and the sires and dams of elite sires.     

Power analysis of QTL detection in half-sib families using selective DNA pooling

Individual loci of economic importance (QTL) can be detected by comparing the inheritance of a trait and the inheritance of loci with alleles readily identifiable by laboratory methods (genetic markers). Data on allele segregation at the individual level are costly and alternatives have been proposed that make use of allele frequencies among progeny, rather than individual genotypes. Among the factors that may affect the power of the set up, the most important are those intrinsic to the QTL: the additive effect of the QTL, and its dominance, and distance between markers and QTL. Other factors are relative to the choice of animals and markers, such as the frequency of the QTL and marker alleles among dams and sires. Data collection may affect the detection power through the size of half-sib families, selection rate within families, and the technical error incurred when estimating genetic frequencies. We present results for a sensitivity analysis for QTL detection using pools of DNA from selected half-sibs. Simulations showed that conclusive detection may be achieved with families of at least 500 half-sibs if sires are chosen on the criteria that most of their marker alleles are either both missing, or one is fixed, among dams.     

Optimal selection on two quantitative trait loci with linkage

A mathematical approach to optimize selection on multiple quantitative trait loci (QTL) and an estimate of residual polygenic effects was applied to selection on two linked or unlinked additive QTL. Strategies to maximize total or cumulative discounted response over ten generations were compared to standard QTL selection on the sum of breeding values for the QTL and an estimated breeding value for polygenes, and to phenotypic selection. Optimal selection resulted in greater response to selection than standard QTL or phenotypic selection. Tight linkage between the QTL (recombination rate 0.05) resulted in a slightly lower response for standard QTL and phenotypic selection but in a greater response for optimal selection. Optimal selection capitalized on linkage by emphasizing selection on favorable haplotypes. When the objective was to maximize total response after ten generations and QTL were unlinked, optimal selection increased QTL frequencies to fixation in a near linear manner. When starting frequencies were equal for the two QTL, equal emphasis was given to each QTL, regardless of the difference in effects of the QTL and regardless of the linkage, but the emphasis given to each of the two QTL was not additive. These results demonstrate the ability of optimal selection to capitalize on information on the complex genetic basis of quantitative traits that is forthcoming.     

数量性状基因座位及其在家禽中的定位

近年来随着现代分子生物学的发展 ,一些高效的分子遗传标记将各种畜禽的遗传图谱研究推向深入。为高密度、覆盖面广的连锁图谱的构建及QTL的定位奠定了基础。有关QTL的基本理论、QTL定位的步骤、QTL的检测方法以及家禽中定位的QTL已经展开了深入的研究 ,但目前QTL定位中存在诸多问题的问题     

Optimizing Selection on Multiple Identified Quantitative Trait Loci in Population with Overlapping Generations

A method was developed to model and optimize selection on multiple identified quantitative trait loci (QTLs) and polygenic estimated breeding value, in order to maximize a weighted sum of cumulative response to selection over multiple years in a population with overlapping generations. The model allows for a population with multiple sex-age classes, different number of age class between sires and dams, and varied genetic contribution of the age class. The optimization problem was formulated as a multiple-stage optimal control problem and solved by a forward and backward iteration loop. The practical utility of this method was illustrated in an example of pig breeding population with overlapping generations. The selection response of this method was compared with standard QTL selection and conventional best linear unbiased prediction (BLUP) selection. Simulation results show that optimal selection achieved greater selection response than either standard QTL or conventional BLUP selections. The influence of population structure on optimal selection was significant. Optimal QTL selection and standard QTL selection were more favorable in a population with overlapping generations than discrete generations, and obtained more benefits relative to conventional BLUP selection in a population with overlapping generations. Optimal QTL selection relative to conventional BLUP selection is also more favorable following increase of genetic contribution of two-year-old boars and sows in a population with overlapping generations.     

The distribution of the effects of genes affecting quantitative traits in livestock

Meta-analysis of information from quantitative trait loci (QTL) mapping experiments was used to derive distributions of the effects of genes affecting quantitative traits. The two limitations of such information, that QTL effects as reported include experimental error, and that mapping experiments can only detect QTL above a certain size, were accounted for. Data from pig and dairy mapping experiments were used. Gamma distributions of QTL effects were fitted with maximum likelihood. The derived distributions were moderately leptokurtic, consistent with many genes of small effect and few of large effect. Seventeen percent and 35% of the leading QTL explained 90% of the genetic variance for the dairy and pig distributions respectively. The number of segregating genes affecting a quantitative trait in dairy populations was predicted assuming genes affecting a quantitative trait were neutral with respect to fitness. Between 50 and 100 genes were predicted, depending on the effective population size assumed. As data for the analysis included no QTL of small effect, the ability to estimate the number of QTL of small effect must inevitably be weak. It may be that there are more QTL of small effect than predicted by our gamma distributions. Nevertheless, the distributions have important implications for QTL mapping experiments and Marker Assisted Selection (MAS). Powerful mapping experiments, able to detect QTL of 0.1σ_p, will be required to detect enough QTL to explain 90% the genetic variance for a quantitative trait.     

世代重叠群体多个QTL最优化选择

一种扩展的方法能够在一个世代重叠的群体内对多个数量性状位点选择进行最优化,目的是为了在整个计划期内获得最大的累积反应加权和。该模型允许群体有多个性别年龄组、公母畜间有不同的年龄组数、各年龄组有不同的遗传贡献。整个最优化问题被描述成一个多阶段系统优化控制问题,通过一个向前和向后的迭代循环解决。用一个世代重叠的实际育种猪群的参数来评价该方法的选择效果,并和标准QTL选择和常规BLUP选择进行比较。模拟结果表明,优化选择要优于标准QTL选择和常规BLUP选择。群体结构对优化选择的影响比较明显。优化QTL选择和标准QTL选择在世代重叠的群体内比在世代离散的群体内的选择优势更明显,相对于常规BLUP选择,能够获得更大的选择优势。在世代重叠群体内随着2岁公畜遗传贡献的增大,优化选择相对于常规BLUP选择的优势越明显。     

Identification of quantitative trait loci affecting resistance to gastrointestinal parasites in a double backcross population of Red Maasai and Dorper sheep

A genome‐wide scan for quantitative trait loci (QTL) affecting gastrointestinal nematode resistance in sheep was completed using a double backcross population derived from Red Maasai and Dorper ewes bred to F₁ rams. This design provided an opportunity to map potentially unique genetic variation associated with a parasite‐tolerant breed like Red Maasai, a breed developed to survive East African grazing conditions. Parasite indicator phenotypes (blood packed cell volume – PCV and faecal egg count – FEC) were collected on a weekly basis from 1064 lambs during a single 3‐month post‐weaning grazing challenge on infected pastures. The averages of last measurements for FEC (AVFEC) and PCV (AVPCV), along with decline in PCV from challenge start to end (PCVD), were used to select lambs (N = 371) for genotyping that represented the tails (10% threshold) of the phenotypic distributions. Marker genotypes for 172 microsatellite loci covering 25 of 26 autosomes (1560.7 cm ) were scored and corrected by Genoprob prior to qxpak analysis that included Box–Cox transformed AVFEC and arcsine transformed PCV statistics. Significant QTL for AVFEC and AVPCV were detected on four chromosomes, and this included a novel AVFEC QTL on chromosome 6 that would have remained undetected without Box–Cox transformation methods. The most significant P‐values for AVFEC, AVPCV and PCVD overlapped the same marker interval on chromosome 22, suggesting the potential for a single causative mutation, which remains unknown. In all cases, the favourable QTL allele was always contributed from Red Maasai, providing support for the idea that future marker‐assisted selection for genetic improvement of production in East Africa will rely on markers in linkage disequilibrium with these QTL.     

Genome-wide scan for bovine twinning rate QTL using linkage disequilibrium

Twinning is a complex trait with negative impacts on health and reproduction, which cause economic loss in dairy production. Several twinning rate quantitative trait loci (QTL) have been detected in previous studies, but confidence intervals for QTL location are broad and many QTL are unreplicated. To identify genomic regions or genes associated with twinning rate, QTL analysis based on linkage combined with linkage disequilibrium (LLD) and individual marker associations was conducted across the genome using high-throughput single nucleotide polymorphism (SNP) genotypes. A total of 9919 SNP markers were genotyped with 200 sires and sons in 19 half-sib North American Holstein dairy cattle families. After SNPs were genotyped, informative markers were selected for genome-wide association tests and QTL searches. Evidence for twinning rate QTL was found throughout the genome. Thirteen markers significantly associated with twinning rate were detected on chromosomes 2, 5 and 14 ( P  < 2.3 × 10⁻⁵). Twenty-six regions on fourteen chromosomes were identified by LLD analysis at P  < 0.0007. Seven previously reported ovulation or twinning rate QTL were supported by results of single marker association or LLD analyses. Single marker association analysis and LLD mapping were complementary tools for the identification of putative QTL in this genome scan.     

性状遗传力与QTL方差对标记辅助选择效果的影响

在采用动物模型标记辅助最佳线性无偏预测方法对个体育种值进行估计的基础上,模拟了在一个闭锁群体内连续对单个性状选择10个世代的情形,并系统地比较了性状遗传力和QTL方差对标记辅助选择所获得的遗传进展、QTL增效基因频率和群体近交系数变化的影响。结果表明：在对高遗传力和QTL方差较小的性状实施标记辅助选择时,可望获得更大的遗传进展;遗传力越高,QTL方差越大,则QTL增效基因频率的上升速度越快;遗传力较高时,群体近交系数上升的速度较为缓慢,而QTL方差对群体近交系数上升速度的影响则不甚明显。结合前人关于标记辅助选择相对效率的研究结果,可以认为：当选择性状的遗传力和QTL方差为中等水平时,标记辅助选择可望获得理想的效果。     

Refinement of two female fertility QTL using alternative phenotypes in French Holstein dairy cattle

Two quantitative trait loci (QTL) affecting female fertility were mapped in French dairy cattle. Phenotypes were non-return rates at 28, 56, 90 and 282 days after insemination. On chromosome 3, a QTL was significant at 1% for non-return rate at 90 days, suggesting that it affects early fertility events. An analysis of SLC35A3, which causes complex vertebral malformation, excluded this gene from the QTL interval. On chromosome 7, a QTL was almost significant (P = 0.05) for non-return rate at 282 days. This QTL was associated with abortion and stillbirth problems. Use of appropriate phenotypes appeared important for fine-mapping QTL associated with fertility.     

Verification of yield QTL through realized molecular marker- assisted selection responses in a barley cross

Verification of putative quantitative trait loci (QTL) is an essential step towards implementing the use of marker-assisted selection (MAS) in cultivar improvement. In a previous study with 150 doubled haploid lines derived from the 6-row cross Steptoe/Morex (S/M), four regions (QTL1–4) of the barley genome were associated with differential genotypic expression for grain yield across environments. The objectives of this study were to verify the value of these four QTL for selection and to compare the efficiency of alternative MAS strategies using these QTL vs. conventional phenotypic selection for grain yield. A total of 92 DHLs derived from the S/M cross that were not used in the original mapping efforts were used for QTL verification. Confirmation of QTL effects was first accomplished by assessing yield differences between individuals carrying alternative alleles at each putative locus in three environments. QTL1 on chromosome 3 was confirmed as the most important and consistent locus to determine yield across sites, with the S allele being favorable. The M allele at QTL3 on chromosome 6 was beneficial for grain yield across sites, but to a lesser degree than QTL1. Magnitudes of allele effects at QTL2 (chromosome 2) and QTL4 (chromosome 7) were highly influenced by the environment where the genotypes were grown. Verification of QTL effects was best achieved by comparing realized selection response. Genotypic (MAS) and tandem genotypic and phenotypic selection were at least as good as phenotypic selection. Consistent selection responses were detected for QTL1 alone and together with QTL3. Genotypic selection for lines carrying the S allele at QTL1 resulted in the identification of high-yielding genotypes. Selection responses increased when the M allele at QTL3 was combined with the S allele at QTL1. Significant qualitative QTL × environment interactions for QTL2 and QTL4 were detected through differential realized selection responses at different sites. Without a thorough understanding of the physiological and agronomic particulars of any QTL and the target environment, MAS for QTL showing qualitative interactions should be minimized This revised version was published online in June 2006 with corrections to the Cover Date.     

Ultra-simple DNA extraction method for marker-assisted selection using microsatellite markers in rice

We prevent an ultra-simple DNA extraction method for microsatellite analysis of rice. Each extraction requires only one microtube, one disposable pipette tip, TE buffer and few pieces (about 5 mm) of rice leaf tissue. This is sufficient for 200 PCR reactions. The extract can be kept in the freezer for long-term storage. Also, DNA can be extracted from 200–300 individuals in a few hours. These features enabled us to perform rapid largescale seedling genotyping required for marker-assisted selection. We have also examined the applicability of this method for other PCR-based markers: RAPDs, nuclear STS, chloroplast STS and chloroplast microsatellites.     

Molecular marker-assisted selection for malting quality traits in barley

Selection for malting quality in breeding programs by micromalting and micromashing is time-consuming, and resource-intensive. More efficient and feasible approaches for identifying genotypes with good malting quality would be highly desirable. With the advent of molecular markers, it is possible to map and tag the loci affecting malting quality. The objective of this study was to assess the effectiveness of molecular marker assisted selection for malting quality traits. Two major quantitative trait loci (QTL) regions in six-row barley for malt extract percentage, -amylase activity, diastatic power, and malt -glucan content on chromosomes 1 (QTL1) and 4 (QTL2) have been previously identified. The flanking markers, Brz and Amy2, and WG622 and BCD402B, for these two major QTL regions were used in marker-assisted selection. Four alternative selection strategies; phenotypic selection, genotypic selection, tandem genotypic and phenotypic selection, and combined phenotypic and genotypic selection, were compared for both single and multiple trait selection in a population consisting of 92 doubled haploid lines derived from Steptoe × Morex crosses. Marker assisted selection for QTL1 (tandem genotypic and phenotypic selection, and combined phenotypic and genotypic selection) was more effective than phenotypic selection, but for QTL2 was not as effective as phenotypic selection due to a lack of QTL2 effects in the selection population. The effectiveness of tandem genotypic and phenotypic selection makes marker assisted selection practical for traits which are extremely difficult or expensive to measure such as most malting quality traits. It can substantially eliminate undesirable genotypes by early genotyping and keeping only desirable genotypes for later phenotypic selection.     

Detection of QTL for immune response to sheep red blood cells in laying hens

The aim of this study is to detect quantitative trait loci (QTL) involved in the regulation of the primary and the secondary immune response to sheep red blood cells (SRBC) in a resource population using microsatellite DNA markers. The F2 resource population originates from a cross of two divergently selected lines for either high (H line) or low (L line) primary antibody response to SRBC. The F2 population consisted of six half-sib families, three families per each of reciprocal crosses. Total antibody titres to SRBC were determined by agglutination in serum from all birds. F2, F1 and F0 generations were genotyped for 170 microsatellite markers, using a whole-genome scan approach. The half-sib and the line-cross analyses were performed to determine QTL regions associated with regulation of the immune response. In the half-sib analysis, four QTL for SRBC primary response have been identified: on GGA3, GGA5, GGA16 and GGA23. No QTL was identified for SRBC secondary response under the half-sib model. In the line-cross analysis, three QTL were identified on GGA10, GGA16 and GGA27 for SRBC primary response and five QTL were identified on GGA6, GGA9, GGA15, GGA16 and GGA27 for SRBC secondary response. Subsequently, the family contribution of individual families to the QTL was analysed. The family with the largest contribution was genotyped with additional microsatellite markers in the QTL region on GGA5. The extended half-sib analysis with additional genotype information results in narrowing down the QTL region on GGA5.     

家禽数量性状基因座定位的研究进展

近二十年来,各种DNA标记技术及相关生物技术的发展和完善为高密度、覆盖面广的连锁图谱的构建及QTL的定位奠定了基础,本就目前世界上建立的几个较有影响的资源家系、各种DNA标记技术、家禽中定位的QTL及存在问题等方面作一综述。     

Marker assisted selection with optimised contributions of the candidates to selection

The benefits of marker assisted selection (MAS) are evaluated under realistic assumptions in schemes where the genetic contributions of the candidates to selection are optimised for maximising the rate of genetic progress while restricting the accumulation of inbreeding. MAS schemes were compared with schemes where selection is directly on the QTL (GAS or gene assisted selection) and with schemes where genotype information is not considered (PHE or phenotypic selection). A methodology for including prior information on the QTL effect in the genetic evaluation is presented and the benefits from MAS were investigated when prior information was used. The optimisation of the genetic contributions has a great impact on genetic response but the use of markers leads to only moderate extra short-term gains. Optimised PHE did as well as standard truncation GAS (i.e. with fixed contributions) in the short-term and better in the long-term. The maximum accumulated benefit from MAS over PHE was, at the most, half of the maximum benefit achieved from GAS, even with very low recombination rates between the markers and the QTL. However, the use of prior information about the QTL effects can substantially increase genetic gain, and, when the accuracy of the priors is high enough, the responses from MAS are practically as high as those obtained with direct selection on the QTL.     

Spatially and temporally varying selection on intrapopulation quantitative trait loci for a life history trade-off in Mimulus guttatus

Why do populations remain genetically variable despite strong continuous natural selection? Mutation reconstitutes variation eliminated by selection and genetic drift, but theoretical and experimental studies each suggest that mutation‐selection balance insufficient to explain extant genetic variation in most complex traits. The alternative hypothesis of balancing selection, wherein selection maintains genetic variation, is an aggregate of multiple mechanisms (spatial and temporal heterogeneity in selection, frequency‐dependent selection, antagonistic pleiotropy, etc.). Most of these mechanisms have been demonstrated for Mendelian traits, but there is little comparable data for loci affecting quantitative characters. Here, we report a 3‐year field study of selection on intrapopulation quantitative trait loci (QTL) of flower size, a highly polygenic trait in Mimulus guttatus. The QTL exhibit antagonistic pleiotropy: alleles that increase flower size, reduce viability, but increase fecundity. The magnitude and direction of selection fluctuates yearly and on a spatial scale of metres. This study provides direct evidence of balancing selection mechanisms on QTL of an ecologically relevant trait.