标记辅助导入的原理与应用

标记辅助导入是分子遗传信息应用于动物育种的一个重要方面, 其目的是在标记信息的辅助下将一个品种(供体)中的一个或多个优良基因导入另一个品种(受体), 同时还要尽可能地保持受体群体原有的遗传背景。在标记辅助导入过程中, 标记信息既可用于辅助前景选择, 即对目标基因携带者的选择, 以保证目标基因的正确导入, 也可用于辅助背景选择, 即对受体基因组的选择, 以加快受体遗传背景的恢复。本文介绍了标记辅助导入的原理和基本方法, 综述了目前已提出的不同前景选择和背景选择方法以及消除遗传累赘(与目标基因连锁的不利基因)的方法, 同时列举了标记辅助导入在动物上的一些成功应用。     

大豆SSR标记辅助遗传背景选择的效果分析

本研究利用鲁豆4号回交转育的大豆种子脂氧酶缺失株系为材料,用IEF-PAGE鉴定大豆种子脂氧酶缺失基因,SSR标记进行遗传背景分析,通过遗传背景回复率相关分析,探索分子标记辅助遗传背景选择时所需的适宜的标记数和选择方式,期望获得可进一步回的鲁豆4号脂氧酶缺失株系。研究明确了大豆SSR标记辅助背景选择时适宜标记数目和选择方式,即先用少数标记初筛,选出遗传背景回复率较高的材料,再用适宜标记鉴定,随着世代递增,已恢复为轮回亲本的标记住点不再分析,逐代减少选择标记数目。获得了合有脂氧酶缺失基因,遗传背景与鲁豆4号差异较小的株系,可用鲁玉4号进一步回交,从而加速培育鲁豆4号脂氧酶缺失近等基因系。     

结合MOET技术的奶牛标记辅助选择方案比较

应用计算机模拟的方法比较利用遗传标记信息和/或超数排卵和胚胎移植(MOET)技术的一系列奶牛育种方案相对于传统育种方案的优越性. 模拟性状为产奶量, QTL作为已知遗传标记. 8个奶牛育种方案分别是：传统的后裔测定方案用STANPT表示; GASPT方案在青年公牛进入后裔测定前通过其自身QTL基因型进行预选择; MOETPT方案应用MOET技术产生青年公牛, 青年公牛预选择为家系内全同胞随机选择; GAMOPT方案结合了QTL预选择及MOET技术; COMBPT方案在GAMOPT方案基础上, 在个体育种值的评估中加入了QTL基因型效应; 另外对应后裔测定体系中MOETPT,GAMOPT,COMBPT方案设计了3个非后裔测定方案, 分别命名为MOET方案、GAMO方案及COMB方案. 动物个体通过相对应的动物模型进行育种值评估, 模拟针对产奶性状进行重叠世代连续17年的选择. 针对现役公牛、泌乳母牛、公牛母亲、公牛父亲和青年公牛5个不同群体, 对应用QTL信息和MOET技术对有利QTL基因频率、真实育种值、多基因值和累积遗传进展优势率产生的影响进行评估. 结果表明, 结合QTL信息和MOET技术的方案, 其真实育种值遗传进展显著高于其他方案, 仅应用QTL信息或MOET技术的单一改进方案间差异不显著, STANPT方案效率最低. 应用MOET技术的方案在第17年获得的多基因选择反应更大. 不同育种方案有利QTL基因频率增加速度在3个公畜群体中差异远大于泌乳母牛群体. GASPT,MOETPT,GAMOPT,COMBPT,MOET,GAMO 和COMB 方案相对STANPT方案, 累积遗传进展优势率在现役公牛群体中分别为8.42%, 3.59%, 14.58%, 18.54%, 4.12%, 14.12%和16.50%, 在泌乳母牛群体中分别为2.70%, 5.00%, 11.05%, 12.78%, 7.51%, 17.12%和25.38%.     

不同QTL增效基因初始频率下标记辅助选择的效果

采用随机模拟方法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。在假定选择性状受一个位于常染色体上的QTL和多基因共同控制的情况下,采用动物模型标记辅助最佳线性无偏预测方法估计个体育种值并据此进行种畜的选留,并在此基础上系统地比较了QTL增效基因初始频率对标记辅助选择效果的影响。结果表明：当群体中QTL增效基因的初始频率较低时,选择所获得的QTL基因型值的进展会更大,标记辅助选择在单位时间内可获得较大的遗传进展;此时,尽管QTL增效基因在群体中固定所需的世代数会更长一些,但其频率上升的速度却更快。而QTL增效基因初始频率的高低对群体近交增量的影响不是很大。     

玉米耐旱功能标记辅助选择初探

干旱是影响玉米生产的主要因素之一,培育耐旱品种可以有效地保持其在干旱环境下的产量稳定性。随着生物信息学数据库的不断完善及基因组学技术的发展,耐旱通用QTL(Quantitative trait locus)的发掘为分子育种提供了新的机遇和方法。本研究在已发掘的耐旱通用QTL基础上,选取相关的18个连锁标记进行开发并且验证在不同种质背景下24份玉米自交系的耐旱性。结果表明,共检测出42个多态性位点,平均多态性信息量为0.4245;通过GGT32(Graphical GenoTypes)图示基因型软件分析SSR位点,得出umc2217、umc2029、phi099、umc1213和phi022这5个连锁标记可用来初步鉴定玉米耐旱性;利用卡方检验,得出phi022和umc2217均达到显著水平,其与耐旱密切相关。因此,这几个连锁标记不仅可被用于相应群体的耐旱分子标记辅助选择,而且为以后的标记辅助选择及抗旱性基因克隆的研究打下基础。     

作物抗旱相关分子标记及其辅助选择的研究进展

分子标记辅助选择育种给作物抗旱育种提供了新的途径。本介绍了国内外在小麦、玉米、水稻、大豆等重要农作物抗旱相关分子标记方面的研究进展。对作物抗旱相关QTL分子标记辅助育种进行了探讨,并对其发展策略提出了一些思考。     

植物抗病育种中的标记辅助选择与甘蔗

抗病基因的分子标记具有稳定、准确、高效的特点,通过对基因型而不是表型的直接选择,抗病基因分子标记应用于辅助选择可大大加快常规育种进程,提高育种效率。本文评述了植物抗病育种中标记辅助选择的发展概况,介绍了各种DNA分子标记技术及植物抗病基因连锁标记的筛选方法,重点介绍了甘蔗抗病基因分子标记研究的现状,展望了分子标记辅助选择在甘蔗抗病育种中的前景。     

利用RAPD技术进行植物性状标记及辅助选择

近等基因系、混合分离群体法是ＲＡＰＤ 标记的主要策略。目前,ＲＡＰＤ标记广泛用于抗线虫、抗病、雄性不育等辅助选择的研究中,取得了可喜的成绩。由于遗传距离的不同,使ＲＡＰＤ 标记具有基因型的差异。寻找无重组的ＲＡＰＤ 标记或将ＲＡＰＤ标记转化为ＲＦＬＰ标记,可以解决这一问题。随着连锁程度的降低选择效率也随着降低。相斥相的ＲＡＰＤ标注可提高选择效率将ＲＡＰＤ标记转化为ＳＣＡＲｓ、ＡＰＳＰｓ 标记,可以解决ＲＡＰＤ 标记稳定性差的问题。来源于ＲＡＰＤ 标记的ＳＣＡＲｓ 标记将在辅助选择中发挥巨大的作用。     

标记辅助选择改良数量性状的研究进展

本系统地介绍了近年来有关标记辅助选择改良数量性状的研究进展,主要包括标记辅助回交、指数选择与最佳线性无偏预测的理论和应用研究概况。理论与计算机模拟表明标记辅助选择比常规表型选择更有效,但在实际育种中并不理想。同时本还就当前标记辅助选择存在的问题和前景进行了讨论。     

利用高代回交和分子标记辅助选择建立水稻单片段代换系

以水稻品种华梗籼74为受体,以6个水稻品种为供体．通过高代回交和微卫星标记辅助选择相结合的方法,建立了水稻的一个单片段代换系群体。该群体Fh86个单片段代换系组成,其中52个在BC3F2中获得,34个在BC3F3中获得。每个单片段代换系只含有来自一个供体的一个染色体代换片段,而遗传背景与华粳籼74相同。这些单片段代换系的代换片段分布于水稻的12条染色体,代换片段的长度为1．5～56．3cM,平均长度为23．0cM。全部代换片段在水稻基因组上的覆盖率为57．1％。     

Comparison of Different Foreground and Background Selection Methods in Marker-Assisted Introgression

Three different methods for foreground selection and four different methods for background selection were compared in terms of the efficiency of marker-assisted introgression of a QTL allele from a donor line into a recipient line and also in terms of the recovery of the recipient genetic background. The results showed that for the introgression of a donor QTL allele, a direct selection on the QTL itself (when the QTL genotype can be directly identified) would ensure that the allele is successfully introgressed and rapidly fixed. However, when a direct selection on the QTL is not feasible, an indirect selection using two closely linked flanking markers can be used, which also shows similar results. For the recovery of the recipient genetic background, if the goal is to recover the whole genetic background of the recipient, genomic similarity selection or marker index selection would be the best choice: Only three generations of backcrosses were required to recover over 98% of the recipient genome. Whereas if the goal is to recover certain background traits of the recipient, MBLUP selection would give the best results, which achieved not only over 99% recovery of the recipient QTL alleles for the background traits after three generations of backcrosses, but also showed the best genetic improvement of these traits.     

Rapid and Targeted Introgression of Genes into Popular Wheat Cultivars Using Marker-Assisted Background Selection

A marker-assisted background selection (MABS)-based gene introgression approach in wheat (Triticum aestivum L.) was optimized, where 97% or more of a recurrent parent genome (RPG) can be recovered in just two backcross (BC) generations. A four-step MABS method was developed based on ‘Plabsim’ computer simulations and wheat genome structure information. During empirical optimization of this method, double recombinants around the target gene were selected in a step-wise fashion during the two BC cycles followed by selection for recurrent parent genotype on non-carrier chromosomes. The average spacing between carrier chromosome markers was <4 cM. For non-carrier chromosome markers that flanked each of the 48 wheat gene-rich regions, this distance was ∼12 cM. Employed to introgress seedling stripe rust (Puccinia striiformis f. sp. tritici) resistance gene Yr15 into the spring wheat cultivar ‘Zak’, marker analysis of 2,187 backcross-derived progeny resulted in the recovery of a BC₂F_2∶3 plant with 97% of the recurrent parent genome. In contrast, only 82% of the recurrent parent genome was recovered in phenotypically selected BC₄F₇ plants developed without MABS. Field evaluation results from 17 locations indicated that the MABS-derived line was either equal or superior to the recurrent parent for the tested agronomic characteristics. Based on these results, MABS is recommended as a strategy for rapidly introgressing a targeted gene into a wheat genotype in just two backcross generations while recovering 97% or more of the recurrent parent genotype.     

Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome

Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F₁ hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.     

Introgression of the avian naked neck gene assisted by DNA fingerprints

Theoretical predictions suggest that DNA markers can be useful tools for genomic selection in gene introgression programmes. An experiment was carried out to evaluate the efficiency of using multi-locus DNA markers in an introgression programme designed to transfer the naked neck gene from a donor to a recipient chicken line. The donor line was a commercial egg layer chicken stock heterozygous at the naked neck locus (Na/na⁺), while the recipients were from a Cornish broiler line. These two lines differ markedly in their average body weight, a quantitative trait that can also represent the comprehensive differences between the genomes of the two lines involved. Three groups of naked neck BC₁ individuals were selected according to the following criteria: (i) low band-sharing with their donor grandsires evaluated by multi-locus DNA markers, (ii) high body weight at six weeks of age, and (iii) selection at random as a control group. Birds from each of these groups were mated at random to individuals from the heavier Cornish line to produce three groups of BC₂ individuals whose body weights were recorded weekly from three to seven weeks of age. Results indicated that BC₂ birds obtained from BC₁ parents selected for band-sharing levels and those selected for body weight, performed equally well at 4–7 weeks of age; both were 3.1–3.9% heavier than birds from the randomly selected group. The additional genome recovery of the heavier broiler line, obtained by DNA markers, was found to be in agreement with theoretically predicted values.     

An Experimental Test of Adaptive Introgression in Locally Adapted Populations of Splash Pool Copepods

As species struggle to keep pace with the rapidly warming climate, adaptive introgression of beneficial alleles from closely related species or populations provides a possible avenue for rapid adaptation. We investigate the potential for adaptive introgression in the copepod, Tigriopus californicus, by hybridizing two populations with divergent heat tolerance limits. We subjected hybrids to strong heat selection for 15 generations followed by whole-genome resequencing. Utilizing a hybridize evolve and resequence (HER) technique, we can identify loci responding to heat selection via a change in allele frequency. We successfully increased the heat tolerance (measured as LT₅₀) in selected lines, which was coupled with higher frequencies of alleles from the southern (heat tolerant) population. These repeatable changes in allele frequencies occurred on all 12 chromosomes across all independent selected lines, providing evidence that heat tolerance is polygenic. These loci contained genes with lower protein-coding sequence divergence than the genome-wide average, indicating that these loci are highly conserved between the two populations. In addition, these loci were enriched in genes that changed expression patterns between selected and control lines in response to a nonlethal heat shock. Therefore, we hypothesize that the mechanism of heat tolerance divergence is explained by differential gene expression of highly conserved genes. The HER approach offers a unique solution to identifying genetic variants contributing to polygenic traits, especially variants that might be missed through other population genomic approaches.     

Introgression and the fate of domesticated genes in a wild mammal population

When domesticated species are not reproductively isolated from their wild relatives, the opportunity arises for artificially selected variants to be re‐introduced into the wild. However, the evolutionary consequences of introgression of domesticated genes back into the wild are poorly understood. By combining high‐throughput genotyping with 25 years of long‐term ecological field data, we describe the occurrence and consequences of admixture between a primitive sheep breed, the free‐living Soay sheep of St Kilda, and more modern breeds. Utilizing data from a 50 K ovine SNP chip, together with forward simulations of demographic scenarios, we show that admixture occurred between Soay sheep and a more modern breed, consistent with historical accounts, approximately 150 years ago. Haplotype‐sharing analyses with other breeds revealed that polymorphisms in coat colour and pattern in Soay sheep arose as a result of introgression of genetic variants favoured by artificial selection. Because the haplotypes carrying the causative mutations are known to be under natural selection in free‐living Soay sheep, the admixture event created an opportunity to observe the outcome of a ‘natural laboratory’ experiment where ancestral and domesticated genes competed with each other. The haplotype carrying the domesticated light coat colour allele was favoured by natural selection, while the haplotype associated with the domesticated self coat pattern allele was associated with decreased survival. Therefore, we demonstrate that introgression of domesticated alleles into wild populations can provide a novel source of variation capable of generating rapid evolutionary changes.     

Coalescence with Background and Balancing Selection in Systems with Bi- and Uniparental Reproduction: Contrasting Partial Asexuality and Selfing

Uniparental reproduction in diploids, via asexual reproduction or selfing, reduces the independence with which separate loci are transmitted across generations. This is expected to increase the extent to which a neutral marker is affected by selection elsewhere in the genome. Such effects have previously been quantified in coalescent models involving selfing. Here we examine the effects of background selection and balancing selection in diploids capable of both sexual and asexual reproduction (i.e., partial asexuality). We find that the effect of background selection on reducing coalescent time (and effective population size) can be orders of magnitude greater when rates of sex are low than when sex is common. This is because asexuality enhances the effects of background selection through both a recombination effect and a segregation effect. We show that there are several reasons that the strength of background selection differs between systems with partial asexuality and those with comparable levels of uniparental reproduction via selfing. Expectations for reductions in N_e via background selection have been verified using stochastic simulations. In contrast to background selection, balancing selection increases the coalescence time for a linked neutral site. With partial asexuality, the effect of balancing selection is somewhat dependent upon the mode of selection (e.g., heterozygote advantage vs. negative frequency-dependent selection) in a manner that does not apply to selfing. This is because the frequency of heterozygotes, which are required for recombination onto alternative genetic backgrounds, is more dependent on the pattern of selection with partial asexuality than with selfing.