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美洲黑杨与小叶杨杂交F1代扦插无性系苗生长性状动态分析
陈玉华, 姚丹, 吴海楠, 陶申童, 吴吉妍, 杨文国, 童春发
南京林业大学学报（自然科学版） ›› 2021, Vol. 45 ›› Issue (1) : 45-52.
PDF(2266 KB)
PDF(2266 KB)
美洲黑杨与小叶杨杂交F1代扦插无性系苗生长性状动态分析
Analyses of dynamic growth traits of the stecklings from the F1 hybrid progeny of Populus deltoides × P. simonii
【目的】探讨美洲黑杨(Populus deltoides)×小叶杨(P. simonii)F1代无性系苗期生长变异,发现F1代无性系生长性状变异规律,为后期在统计分析方面开展杨树数量性状基因定位研究提供重要的参考依据。【方法】以南京林业大学下蜀林场美洲黑杨×小叶杨F1代无性系为研究材料,采用完全随机区组设计,对苗高和地径生长性状在扦插后2年的不同时期进行测量,利用R语言和SPSS统计软件进行遗传变异分析和评价。【结果】苗高和地径在区组间、无性系间、区组与无性系交互作用间均达极显著差异水平。苗高的变异系数2017年由31.96%变为22.04%,2018年稳定在20%左右,地径的变异系数在2017、2018年两个年末分别为26.66%和26.20%。苗高和地径在两年中多个时间点的重复力具有一定波动性,苗高的重复力2017年由0.69逐渐降低到0.41,2018年又回升到近0.60;地径的重复力在2017年末较低,2018年末变为较高的水平(0.59)。根据无性系效应估计值,每年的无性系大致可分为8类,每类的均值效应具有独特的变化趋势,2017年有CL2、CL6、CL7和CL8共4类的均值效应随时间递增,而CL1、CL3、CL4、CL5类则减少;2018年除CL8类的均值效应增加外,其他7类基本是平稳的,但是类间的效应差异较大。【结论】所调查的随机区组无性系试验林的苗高和地径生长变异较大,遗传水平上差异性在不同生长期有其独特性,所建立的杨树无性系随机区组试验林为杨树数量性状基因(QTL)定位研究提供很好的遗传作图材料。
【Objective】 This study aimed to investigate the variation in the growth traits of clones from the F1 progeny of Populus deltoides × P. simonii to facilitate the establishment of statistical models for detecting quantitative trait loci (QTL) using such clonal materials. 【Method】 A randomized block experiment was designed to test clones from the F1 hybrid population. Tree height and ground diameter were measured for each clonal individual at multiple time points in 2017 and 2018. The statistical software SPSS was used to perform the variation analysis of the growth traits with linear mixed models, while an R package was used for a clustering analysis of clonal effects estimated from the linear models. 【Result】 The effects of tree height and ground diameter were significantly different among the blocks, among the clones, and among the interactions of blocks and clones. The phenotypic coefficient of variation for tree height varied from 31.96% to 22.04% in 2017, and this index was maintained at 20% in 2018. The coefficient of variation for ground diameter was 26.66% and 26.20% in 2017 and 2018, respectively. The repeatability of both tree height and ground diameter varied at multiple time points in the two years. The repeatability of tree height gradually decreased from 0.69 to 0.41 in 2017 but increased to nearly 0.60 in 2018. The repeatability of ground diameter was low in 2017 but increased to 0.59 in 2018. According to the estimates of clonal effects at different time points, the clones were roughly clustered into eight groups, in each of which the mean effects varied uniquely over time. The clonal mean effects for the four clusters in 2017 reduced over time, but for the other four clusters, the means increased. Although the mean effects within clusters in 2018 varied smoothly, the differences between clusters expanded. 【Conclusion】 In summary, the tree height and ground diameter of the clones in the randomized block experiment displayed a great variation, especially at the genetic level at different growth stages over the two years. This provides important evidence for creating unique statistical models for mapping QTLs using these clonal experimental materials.
杨树 / 无性系 / 随机区组试验 / 重复力 / 聚类分析 / 苗期动态生长
Populus / clone / randomized block experiment / repeatability / clustering analysis / dynamic growth at steckling stage
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[目的] 为杨树高产低耗高效工业用材新品种选育筛选新种质。[方法] 采用布雷金多性状综合评定法和模糊数学隶属函数值法,系统分析和评价北方型美洲黑杨种质生长及光、水分、养分等关键环境资源利用性状。[结果] 表明:(1)种源间、种源内无性系间在生长、光合、水分和养分利用方面的差异显著或极显著。(2)总叶面积、成叶速率、暗呼吸速率、氮素转移率、生长旺期水分利用效率与北方型美洲黑杨胸径显著或极显著相关。(3)筛选出M6、Q1、Q5、M5、Q7、Q3、M3、Q9等高产型种质,M6、Q1、Q2、M5、Q5、M3、Q4、M2等高产高光效型种质,Q5、Q1、W9、M5、Q7、M6、M3、W2等高产高水分利用型种质,Q9、Q5、Q3、Q8、Q1、M10、Q7、I5高产高养分利用型种质。其中,Q5、M6、Q1、Q2、Q9等无性系兼具生长和对资源(光、水分和养分)的利用优势。[结论] 北方型美洲黑杨遗传变异丰富,为优良种源和种质选择提供了依据;总叶面积、成叶速率、、暗呼吸速率、氮素转移率等5个与生长关系密切的指标可作为种质资源评价的可靠指标;筛选出的优良种质特别是综合表现最优的5个无性系是后续育种工作的有效资源。
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We have mapped quantitative trait loci (QTLs) for commercially important traits (stem growth and form) and an adaptive trait (spring leaf flush) in a Populus F2 generation derived from a cross between interspecific F1 hybrids (P. trichocarpa x P. deltoides). Phenotypic data were collected over a 2-year period from a replicated clonal trial containing ramets of the parental, F1, and F2 trees. Contrary to the assumptions of simple polygenic models of quantitative trait inheritance, 1-5 QTLs of large effect are responsible for a large portion of the genetic variance in each of the traits measured. For example, 44.7% of the genetic variance in stem volume after 2 years of growth is controlled by just two QTLs. QTLs governing stem basal area were found clustered with QTLs for sylleptic branch leaf area, sharing similar chromosomal position and mode of action and suggesting a pleiotropic effect of QTLs ultimately responsible for stem diameter growth.
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We report molecular genetic linkage maps for an interspecific hybrid population of Populus, a model system in forest-tree biology. The hybrids were produced by crosses between P. deltoides (mother) and P. euramericana (father), which is a natural hybrid of P. deltoides (grandmother) and P. nigra (grandfather). Linkage analysis from 93 of the 450 backcross progeny grown in the field for 15 years was performed using random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), and inter-simple sequence repeats (ISSRs). Of a total of 839 polymorphic markers identified, 560 (67%) were testcross markers heterozygous in one parent but null in the other (segregating 1:1), 206 (25%) were intercross dominant markers heterozygous in both parents (segregating 3:1), and the remaining 73 (9%) were 19 non-parental RAPD markers (segregating 1:1) and 54 codominant AFLP markers (segregating 1:1:1:1). A mixed set of the testcross markers, non-parental RAPD markers, and codominant AFLP markers was used to construct two linkage maps, one based on the P. deltoides (D) genome and the other based on P. euramericana (E). The two maps showed nearly complete coverage of the genome, spanning 3801 and 3452 cM, respectively. The availability of non-parental RAPD and codominant AFLP markers as orthologous genes allowed for a direct comparison of the rate of meiotic recombination between the two different parental species. Generally, the rate of meiotic recombination was greater for males than females in our interspecific poplar hybrids. The confounded effect of sexes and species causes the mean recombination distance of orthologous markers to be 11% longer for the father (P. euramericana; interspecific hybrid) than for the mother (P. deltoides; pure species). The linkage maps constructed and the interspecific poplar hybrid population in which clonal replicates for individual genotypes are available present a comprehensive foundation for future genomic studies and quantitative trait locus (QTL) identification.
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The AFLP genetic linkage maps for two poplar cultivars were constructed with the pseudo-test-cross mapping strategy. The hybrids were derived from an interspecific backcross between the female hybrid clone
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BACKGROUND: Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. RESULTS: Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'. CONCLUSION: Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
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Based on a two-way pseudo-testcross strategy, high density and complete coverage linkage maps were constructed for the maternal and paternal parents of an intraspecific F2 pedigree of Populus deltoides. A total of 1,107 testcross markers were obtained, and the mapping population consisted of 376 progeny. Among these markers, 597 were from the mother, and were assigned into 19 linkage groups, spanning a total genetic distance of 1,940.3 cM. The remaining 519 markers were from the father, and were also were mapped into 19 linkage groups, covering 2,496.3 cM. The genome coverage of both maps was estimated as greater than 99.9% at 20 cM per marker, and the numbers of linkage groups of both maps were in accordance with the 19 haploid chromosomes in Populus. Marker segregation distortion was observed in large contiguous blocks on some of the linkage groups. Subsequently, we mapped the segregation distortion loci in this mapping pedigree. Altogether, eight segregation distortion loci with significant logarithm of odds supports were detected. Segregation distortion indicated the uneven transmission of the alternate alleles from the mapping parents. The corresponding genome regions might contain deleterious genes or be associated with hybridization incompatibility. In addition to the detection of segregation distortion loci, the established genetic maps will serve as a basic resource for mapping genetic loci controlling traits of interest in future studies.
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Deciphering the genetic architecture underlying polygenic traits in perennial species can inform molecular marker-assisted breeding. Recent advances in high-throughput sequencing have enabled strategies that integrate linkage-linkage disequilibrium (LD) mapping in Populus. We used an integrated method of quantitative trait locus (QTL) dissection with a high-resolution linkage map and multi-gene association mapping to decipher the nature of genetic architecture (additive, dominant, and epistatic effects) of potential QTLs for growth traits in a Populus linkage population (1200 progeny) and a natural population (435 individuals). Seventeen QTLs for tree height, diameter at breast height, and stem volume mapped to 11 linkage groups (logarithm of odds (LOD) >/= 2.5), and explained 2.7-18.5% of the phenotypic variance. After comparative mapping and transcriptome analysis, 187 expressed genes (10 046 common single nucleotide polymorphisms (SNPs)) were selected from the segmental homology regions (SHRs) of 13 QTLs. Using multi-gene association models, we observed 202 significant SNPs in 63 promising genes from 10 QTLs (P
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BACKGROUND: Restriction site associated DNA sequencing (RAD-seq), a next-generation sequencing technology, has greatly facilitated genetic linkage mapping studies in outbred species. RAD-seq is capable of discovering thousands of genetic markers for linkage mapping across many individuals, and can be applied in species with or without a reference genome. Although several analytical tools are available for RAD-seq data, alternative strategies are necessary for improving the marker quality and hence the genetic mapping accuracy. RESULTS: We demonstrate a strategy for constructing dense genetic linkage maps in hybrid forest trees by combining RAD-seq and whole-genome sequencing technologies. We performed RAD-seq of 150 progeny and whole-genome sequencing of the two parents in an F1 hybrid population of Populus deltoides x P. simonii. Two rough references were assembled from the whole-genome sequencing reads of the two parents separately. Based on the parental reference sequences, 3442 high-quality single nucleotide polymorphisms (SNPs) were identified that segregate in the ratio of 1:1. The maternal linkage map of P. deltoides was constructed with 2012 SNPs, containing 19 linkage groups and spanning 4067.16 cM of the genome with an average distance of 2.04 cM between adjacent markers, while the male map of P. simonii consisted of 1430 SNPs and the same number of linkage groups with a total length of 4356.04 cM and an average interval distance of 3.09 cM. Collinearity between the parental linkage maps and the reference genome of P. trichocarpa was also investigated. Compared with the result on the basis of the existing reference genome, our strategy identified more high-quality SNPs and generated parental linkage groups that nicely match the karyotype of Populus. CONCLUSIONS: The strategy of simultaneously using RAD and whole-genome sequencing technologies can be applied to constructing high-density genetic maps in forest trees regardless of whether a reference genome exists. The two parental linkage maps constructed here provide more accurate genetic resources for unraveling quantitative trait loci and accelerating molecular breeding programs, as well as for comparative genomics in Populus.
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The advent of complete genetic linkage maps consisting of codominant DNA markers [typically restriction fragment length polymorphisms (RFLPs)] has stimulated interest in the systematic genetic dissection of discrete Mendelian factors underlying quantitative traits in experimental organisms. We describe here a set of analytical methods that modify and extend the classical theory for mapping such quantitative trait loci (QTLs). These include: (i) a method of identifying promising crosses for QTL mapping by exploiting a classical formula of SEWALL WRIGHT; (ii) a method (interval mapping) for exploiting the full power of RFLP linkage maps by adapting the approach of LOD score analysis used in human genetics, to obtain accurate estimates of the genetic location and phenotypic effect of QTLs; and (iii) a method (selective genotyping) that allows a substantial reduction in the number of progeny that need to be scored with the DNA markers. In addition to the exposition of the methods, explicit graphs are provided that allow experimental geneticists to estimate, in any particular case, the number of progeny required to map QTLs underlying a quantitative trait.
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| [34] |
Adequate separation of effects of possible multiple linked quantitative trait loci (QTLs) on mapping QTLs is the key to increasing the precision of QTL mapping. A new method of QTL mapping is proposed and analyzed in this paper by combining interval mapping with multiple regression. The basis of the proposed method is an interval test in which the test statistic on a marker interval is made to be unaffected by QTLs located outside a defined interval. This is achieved by fitting other genetic markers in the statistical model as a control when performing interval mapping. Compared with the current QTL mapping method (i.e., the interval mapping method which uses a pair or two pairs of markers for mapping QTLs), this method has several advantages. (1) By confining the test to one region at a time, it reduces a multiple dimensional search problem (for multiple QTLs) to a one dimensional search problem. (2) By conditioning linked markers in the test, the sensitivity of the test statistic to the position of individual QTLs is increased, and the precision of QTL mapping can be improved. (3) By selectively and simultaneously using other markers in the analysis, the efficiency of QTL mapping can be also improved. The behavior of the test statistic under the null hypothesis and appropriate critical value of the test statistic for an overall test in a genome are discussed and analyzed. A simulation study of QTL mapping is also presented which illustrates the utility, properties, advantages and disadvantages of the method.
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| [35] |
Simple statistical methods for the study of quantitative trait loci (QTL), such as analysis of variance, have given way to methods that involve several markers and high-resolution genetic maps. As a result, the mapping community has been provided with statistical and computational tools that have much greater power than ever before for studying and locating multiple and interacting QTL. Apart from their immediate practical applications, the lessons learnt from this evolution of QTL methodology might also be generally relevant to other types of functional genomics approach that are aimed at the dissection of complex phenotypes, such as microarray assessment of gene expression.
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| [36] |
Statistical methods for mapping quantitative trait loci (QTLs) in full-sib forest trees, in which the number of alleles and linkage phase can vary from locus to locus, are still not well established. Previous studies assumed that the QTL segregation pattern was fixed throughout the genome in a full-sib family, despite the fact that this pattern can vary among regions of the genome. In this paper, we propose a method for selecting the appropriate model for QTL mapping based on the segregation of different types of markers and QTLs in a full-sib family. The QTL segregation patterns were classified into three types: test cross (1:1 segregation), F(2) cross (1:2:1 segregation) and full cross (1:1:1:1 segregation). Akaike's information criterion (AIC), the Bayesian information criterion (BIC) and the Laplace-empirical criterion (LEC) were used to select the most likely QTL segregation pattern. Simulations were used to evaluate the power of these criteria and the precision of parameter estimates. A Windows-based software was developed to run the selected QTL mapping method. A real example is presented to illustrate QTL mapping in forest trees based on an integrated linkage map with various segregation markers. The implications of this method for accurate QTL mapping in outbred species are discussed.
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| [37] |
Linkage disequilibrium (LD) mapping using natural populations results in higher resolution of marker-trait associations compared to family-based quantitative trait locus (QTL) studies. Depending on the extent of LD, it is possible to identify alleles within candidate genes associated with a trait. Analysis of a natural mutant in Arabidopsis has shown that mutations in cinnamoyl CoA reductase (CCR), a key lignin gene, affect physical properties of the secondary cell wall such as stiffness and strength. Using this gene, we tested whether LD mapping could identify alleles associated with microfibril angle (MFA), a wood quality trait affecting stiffness and strength of wood. We identified 25 common single-nucleotide polymorphism (SNP) markers in the CCR gene in Eucalyptus nitens. Using single-marker and haplotype analyses in 290 trees from a E. nitens natural population, two haplotypes significantly associated with MFA were found. These results were confirmed in two full-sib families of E. nitens and Eucalyptus globulus. In an effort to understand the functional significance of the SNP markers, we sequenced the cDNA clones and identified an alternatively spliced variant from the significant haplotype region. This study demonstrates that LD mapping can be used to identify alleles associated with wood quality traits in natural populations of trees.
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| [38] |
Genetic association is a powerful method for dissecting complex adaptive traits due to (i) fine-scale mapping resulting from historical recombination, (ii) wide coverage of phenotypic and genotypic variation within a single experiment, and (iii) the simultaneous discovery of loci and alleles. In this article, genetic association among single nucleotide polymorphisms (58 SNPs) from 20 wood- and drought-related candidate genes and an array of wood property traits with evolutionary and commercial importance, namely, earlywood and latewood specific gravity, percentage of latewood, earlywood microfibril angle, and wood chemistry (lignin and cellulose content), was tested using mixed linear models (MLMs) that account for relatedness among individuals by using a pairwise kinship matrix. Population structure, a common systematic bias in association studies, was assessed using 22 nuclear microsatellites. Different phenotype:genotype associations were found, some of them confirming previous evidence from collocation of QTL and genes in linkage maps (for example, 4cl and percentage of latewood) and two that involve nonsynonymous polymorphisms (cad SNP M28 with earlywood specific gravity and 4cl SNP M7 with percentage of latewood). The strongest genetic association found in this study was between allelic variation in alpha-tubulin, a gene involved in the formation of cortical microtubules, and earlywood microfibril angle. Intragenic LD decays rapidly in conifers; thus SNPs showing genetic association are likely to be located in close proximity to the causative polymorphisms. This first multigene association genetic study in forest trees has shown the feasibility of candidate gene strategies for dissecting complex adaptive traits, provided that genes belonging to key pathways and appropriate statistical tools are used. This approach is of particular utility in species such as conifers, where genomewide strategies are limited by their large genomes.
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| [39] |
杜庆章. 利用连锁与连锁不平衡联合作图解析毛白杨重要性状的等位遗传变异[D]. 北京: 北京林业大学, 2014.
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