染色体片段导入系在作物遗传育种研究中的应用

染色体片段导入系是在轮回亲本的遗传背景上只含有一个或少量供体染色体片段的家系,可作为QTL分析的重要材料。在QTL检测时,染色体片段导入系的遗传背景清楚,可有效检测微效基因及隐蔽基因,准确地评价供体染色体片段的遗传效应,打破优良基因与不良基因的连锁,提高QTL检测的效率和准确性。另外,染色体片段导入系不仅可用于QTL精细定位和基因克隆、QTL间互作、QTL与环境互作以及杂种优势的研究,同时还可用于作物聚合育种和分子设计育种。本文对染色体片段导入系的构建及其在作物遗传育种中的应用进展进行了综述。     

基于掖478导入系的玉米百粒重QTL鉴定

玉米百粒重是产量性状的主要组成因子,对其控制位点进行QTL鉴定或基因克隆,将有益于其遗传控制的研究和分子育种的实施。本研究以导入系SL19-41为材料,该导入系是以我国玉米育种中广泛应用的骨干自交系掖478(Ye478)为遗传背景导入QB80染色体片段的纯合系。使用该导入系与Ye478杂交构建分离群体(F2、F2:3家系和BC1F1),通过3个环境下的田间试验,利用Ici Mapping的逐步回归区间作图法进行百粒重QTL定位,以及进行QTL位点连锁标记的表型效应分析。结果表明:鉴定了2个百粒重QTL位点,其中位于第4染色体bnlg1784~umc1194区间QTL位点q KW4-1在3个环境下均被检测到,可解释的表型变异为6.74%~17.81%,阐明了导入系SL19-41百粒重性状的遗传机制,同时也获得了改良版的Ye478(Ye478QB80),为玉米百粒重的遗传改良提供有益的分子标记,也为克隆百粒重基因提供材料来源。     

基于染色体置换系的野生稻抽穗期及紫色性状QTL的鉴定

利用一套以9311为背景的普通野生稻染色体片段置换系群体为研究材料,进行野生稻相关QTL的定位与基因的鉴定。在多年多点的抽穗期调查数据基础上,结合200多个分子标记引物的基因型鉴定结果,定位到11个与抽穗期相关的QTL;选取携带相关QTL导入片段的两个置换系进一步研究,发现2个抽穗期主效QTL均为已克隆基因的等位基因。利用叶鞘、稃尖、柱头颜色与9311差异显著的一个单片段置换系定位到来自野生稻的紫色性状基因Or C,初步鉴定与栽培稻的等位基因功能不同。这些结果再次表明染色体片段置换系是行之有效的QTL定位以及基因发掘的遗传群体。通过对抽穗期、紫色性状相关QTL的定位与基因的鉴定,为进一步的功能研究提供了基因资源。     

基于玉米导入系群体的3个农艺性状QTL分析

通过回交育种程序结合SSR标记构建以玉米自交系农系531为受体亲本、10个具有不同农艺性状的自交系为供体的染色体片段导入系群体,在该群体BC3F3世代,利用GGT32图示基因型软件和Windows QTL IciMapping v1.0对导入片段进行检测、并结合田间调查对控制玉米穗位高、穗上叶夹角和株高的QTL进行分析.研究表明,导入系群体的创建在遗传结构上改良了农系531穗位偏高、穗上叶夹角偏大的不足,并得到基本符合育种目标的改良株系.通过QTL分析,在具有相同性状改良的单株上,分别检测到4个包含穗位高、4个包含穗上叶夹角和6个包含株高QTL的共同的导入染色体片段.     

茶陵野生稻导入系遗传分析及重要性状相关QTL鉴定

普通野生稻是栽培稻的祖先种,从野生稻中挖掘栽培稻中已丢失或削弱了的优异基因是保证水稻高产稳产的一个重要手段。本研究以茶陵野生稻染色体片段导入系群体为研究材料,使用均匀分布于12条水稻染色体上的136个多态性分子标记,对其遗传背景进行检测。平均每个导入系携带24个导入片段,导入片段平均长度为16.1 cM,导入片段覆盖野生稻基因组的87.89%。结合两个环境中的性状调查,鉴定到与6个产量性状相关的18个QTLs,其中6号染色体上与粒宽有关的QTL在两个环境中被连续检测到。除此之外,还鉴定到5个与发芽期耐冷性有关的QTLs。     

利用RIL和CSSL群体检测水稻种子休眠性QTL

利用由梗稻品种Asominori与籼稻品种IR24的杂交组合衍生的重组自交F10。家系(Recombinant Inbred Lines,RIL)群体及其衍生的染色体片段置换系(Chromosome Segment Substitution Lines,CSSL)群体,进行了种子休眠性QTL的检测和遗传效应分析。其中CSSL群体有2个,即CSSLl(以Asominori为背景,置换片段来自IR24)和CSSL2(以IR24为背景,置换片段来自Asominori)。在RIL群体上共检测到3个种子休眠性QTL,分别位于第3、6和9染色体上;在CSSL1群体中检测到分布在第1、3和7染色体上的3个休眠性QTL;而在CSSl2群体上检测到的3个QTL则分别位于第1、2和7染色体上。同时在两套CSSL群体上,分别检测到位于第1、7染色体上位置相近且效应一致的休眠性QTL,分析表明其所在的Asominori片段含对种子休眠性的增效基因,相应的IB24段含有减效基因。     

玉米花期耐旱导入系群体的构建与评价

以黄早四X齐319回交群体（BC2F1）为试验材料,在花期进行高强度干旱胁迫和耐旱导入系筛选,获得花期耐旱性显著高于亲本材料的玉米耐旱导入系。利用分子标记对其导入片段进行分析结果表明,在全基因组范围内,耐旱群体在36．59％的位点上含有供体亲本的特异标记,尤其在第4、5染色体上分别达到63．94％、56％,显著高于群体平均值;同时发现,导入频率的提高主要集中于染色体的部分区段,其中部分基因组区域与已定位的耐旱性相关QTL相邻或重叠。     

基于染色体片段导入系发掘抗玉米丝黑穗病主效QTL

选用抗玉米丝黑穗病自交系Mo17和SH15为供体,与受体感病自交系黄早四和昌7-2构建回交群体(BC3F1\BC4F2),通过田间人工接种玉米丝黑穗病原菌鉴定抗病性表现,评价群体抗病性。研究结果显示黄早四×(黄早四×Mo17)BC4F2群体发病率明显高于BC3F1群体;两个BC4F2黄早四×(黄早四×Mo17)和昌7-2×(昌7-2×SH15)群体的发病率差异较大。采用SSR标记分析抗病株的供体染色体导入片段,发现随着回交次数的增多,导入片段数量减少,但不同回交群体中供体导入片段数目明显不同。通过连锁不平衡分析,在染色体2.09和3.04区段发掘和验证2个抗玉米丝黑穗病主效QTL,连锁标记分别为umc2077和phio53或bnlg1965。本文研究结果为抗丝黑穗病基因精细定位和分子聚合育种提供了信息和材料。     

基于CSSL的水稻穗颈长度QTL的代换作图

水稻穗颈长度是影响杂交水稻制种产量提高的重要农艺性状之一。文章利用94个以籼稻品种9311为遗传背景、粳稻品种日本晴为染色体片段供体的覆盖全基因组的染色体片段置换系(Chromosome segment substi-tution lines, CSSL)为材料, 调查和分析CSSL群体及双亲的穗颈长度。结果表明: 在17个置换系中检测到8个控制水稻穗颈长度的数量性状位点(Quantitative trait loci, QTL), 分别位于第2、3、7、8、9和第11染色体; 利用代换作图法, 定位了其中的7个穗颈长度QTL; 其加性效应值介于0.10~3.20之间, 其中qPE-9和qPE-11的加性效应值较大, 平均效应值分别为3.15和2.95, 表现为主效基因特征; qPE-2-2、qPE-3-1、qPE-3-2、qPE-7和qPE-8等5个QTL被定位在小于10.0 cM的区段内。利用CSSL可以有效地鉴定水稻穗颈长度QTL, 这些QTL为分子标记辅助选育穗颈长度适中的水稻品系及其进一步的精细定位奠定了基础。     

基于CSSL的水稻抽穗期QTL定位及遗传分析

抽穗期是水稻(Oryza sativa)品种的重要农艺性状之一, 适宜的抽穗期是获得理想产量的前提。鉴定和定位水稻抽穗期基因/QTL, 分析其遗传效应对改良水稻抽穗期至关重要。以籼稻品种9311(Oryza sativa ssp. indica ‘Yangdao 6’)为受体,粳稻品种日本晴(Oryza sativa ssp. japonica ‘Nipponbare’)为供体构建的94个染色体片段置换系群体为材料, 以P≤0.01为阈值, 对置换片段上的抽穗期QTL进行了鉴定。采用代换作图法共定位了4个控制水稻抽穗期的QTL, 分别位于第3、第4、第5和第8染色体; QTL的加性效应值变化范围为–6.4 – –2.7, 加性效应百分率变化范围为–6.4%– –2.7%; qHD-3和qHD-8加性效应值较大, 表现主效基因特征。为了进一步定位qHD-3和qHD-8, 在目标区域加密16对SSR引物, qHD-3和qHD-8分别被界定在第3染色体RM3166–RM16206之间及第8染色体RM4085-RM8271之间, 其遗传距离分别为13.9 cM和6.4 cM。研究结果为利用分子标记辅助选择改良水稻抽穗期奠定了基础。     

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

Adaptation from standing genetic variation or recurrent de novo mutation in large populations should commonly generate soft rather than hard selective sweeps. In contrast to a hard selective sweep, in which a single adaptive haplotype rises to high population frequency, in a soft selective sweep multiple adaptive haplotypes sweep through the population simultaneously, producing distinct patterns of genetic variation in the vicinity of the adaptive site. Current statistical methods were expressly designed to detect hard sweeps and most lack power to detect soft sweeps. This is particularly unfortunate for the study of adaptation in species such as Drosophila melanogaster, where all three confirmed cases of recent adaptation resulted in soft selective sweeps and where there is evidence that the effective population size relevant for recent and strong adaptation is large enough to generate soft sweeps even when adaptation requires mutation at a specific single site at a locus. Here, we develop a statistical test based on a measure of haplotype homozygosity (H12) that is capable of detecting both hard and soft sweeps with similar power. We use H12 to identify multiple genomic regions that have undergone recent and strong adaptation in a large population sample of fully sequenced Drosophila melanogaster strains from the Drosophila Genetic Reference Panel (DGRP). Visual inspection of the top 50 candidates reveals that in all cases multiple haplotypes are present at high frequencies, consistent with signatures of soft sweeps. We further develop a second haplotype homozygosity statistic (H2/H1) that, in combination with H12, is capable of differentiating hard from soft sweeps. Surprisingly, we find that the H12 and H2/H1 values for all top 50 peaks are much more easily generated by soft rather than hard sweeps. We discuss the implications of these results for the study of adaptation in Drosophila and in species with large census population sizes.     

Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology

There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases.     

The genetic structure of the Raleigh natural population of Drosophila melanogaster revisited

The Raleigh natural population of Drosophila melanogaster was reanalyzed with special attention to possible dysgenic effects during the extraction of chromosomes. About 600 second chromosomes were extracted from the Raleigh natural population, half in the cytoplasm of wild-caught females (native genetic background) and half in the cytoplasm of the laboratory line, C160(In(2LR)SM1, Cy/In(2LR)bw(V1)) (foreign genetic background). We could not find significant differences between the two extraction schemes in the frequency of lethal second chromosomes (Q = 0.252 for the lines with the negative genetic background vs. 0.231 for the lines with the foreign genetic background) or in the homozygous detrimental (D) and lethal (L) loads (D = 0.210 vs. 0.251; L = 0.287 vs. 0.264). The effective size of the population was estimated to be approximately 19,000, based on the allelism rate of lethal-bearing chromosomes. The homozygous load markedly decreased in the 15 years since a previous study of the same population.     

Soft sweeps: molecular population genetics of adaptation from standing genetic variation

A population can adapt to a rapid environmental change or habitat expansion in two ways. It may adapt either through new beneficial mutations that subsequently sweep through the population or by using alleles from the standing genetic variation. We use diffusion theory to calculate the probabilities for selective adaptations and find a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation. We then determine the parameter regions where each scenario-standing variation vs. new mutations-is more likely. Adaptations from the standing genetic variation are favored if either the selective advantage is weak or the selection coefficient and the mutation rate are both high. Finally, we analyze the probability of "soft sweeps," where multiple copies of the selected allele contribute to a substitution, and discuss the consequences for the footprint of selection on linked neutral variation. We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high.     

The Heterogeneous HLA Genetic Makeup of the Swiss Population

THIS STUDY AIMS AT INVESTIGATING THE HLA MOLECULAR VARIATION ACROSS SWITZERLAND IN ORDER TO DETERMINE POSSIBLE REGIONAL DIFFERENCES, WHICH WOULD BE HIGHLY RELEVANT TO SEVERAL PURPOSES: optimizing donor recruitment strategies in hematopoietic stem cell transplantation (HSCT), providing reliable reference data in HLA and disease association studies, and understanding the population genetic background(s) of this culturally heterogeneous country. HLA molecular data of more than 20,000 HSCT donors from 9-13 recruitment centers of the whole country were analyzed. Allele and haplotype frequencies were estimated by using new computer tools adapted to the heterogeneity and ambiguity of the data. Non-parametric and resampling statistical tests were performed to assess Hardy-Weinberg equilibrium, selective neutrality and linkage disequilibrium among different loci, both in each recruitment center and in the whole national registry. Genetic variation was explored through genetic distance and hierarchical analysis of variance taking into account both geographic and linguistic subdivisions in Switzerland. The results indicate a heterogeneous genetic makeup of the Swiss population: first, allele frequencies estimated on the whole national registry strongly deviate from Hardy-Weinberg equilibrium, by contrast with the results obtained for individual centers; second, a pronounced differentiation is observed for Ticino, Graubünden, and, to a lesser extent, Wallis, suggesting that the Alps represent(ed) a barrier to gene flow; finally, although cultural (linguistic) boundaries do not represent a main genetic differentiation factor in Switzerland, the genetic relatedness between population from south-eastern Switzerland and Italy agrees with historical and linguistic data. Overall, this study justifies the maintenance of a decentralized donor recruitment structure in Switzerland allowing increasing the genetic diversity of the national-and hence global-donor registry. It also indicates that HLA data of local donor recruitment centers can be used as reference data in both epidemiological and population genetic studies focusing on the genetic history of present European populations.     

Population continuity or replacement? A novel computer simulation approach and its application to the numic expansion (Western Great Basin,USA)

In a previous study, Kaestle and Smith [Am J Phys Anthropol 115 (2001) 1-12] supported a recent (A.D. 1000) Numic expansion into the Great Basin region based on a molecular and statistical analysis of mitochondrial DNA (mtDNA) of ancient and modern native inhabitants of the region. Their statistical methodology could not rule out the possibility that observed differences in haplogroup frequencies are instead the result of long-term microevolutionary change within a single population. To distinguish more effectively between a Numic expansion versus population continuity, we employed a novel computer simulation approach that incorporates microevolutionary factors likely to affect human population genetic variation. We test whether the observed differences in haplogroup frequencies between ancient and modern Great Basin groups could have been produced solely via in situ microevolutionary change. Our results indicate that for reasonable demographic conditions, the observed genetic differences between the observed samples are consistent with population continuity if gene flow among prehistoric Great Basin local groups was less than 1% of local group size per generation. Our analysis also supports a recent population expansion if gene flow between neighboring groups exceeded 8% of local group size per generation. The simulations demonstrate that relatively low gene flow levels and random genetic drift can produce the observed degree of genetic differences between population samples. Although this study focuses on the Numic expansion, this simulation approach can be applied to any geographic region for which genetic data have been collected to address similar questions of population relationships over time.     

Maximum-likelihood estimation of gene location by linkage disequilibrium.

Linkage disequilibrium, D, between a polymorphic disease and mapped markers can, in principle, be used to help find the map position of the disease gene. Likelihoods are therefore derived for the value of D conditional on the observed number of haplotypes in the sample and on the population parameter Nc, where N is the effective population size and c the recombination fraction between the disease and marker loci. The likelihood is computed explicitly for the case of two loci with heterozygote superiority and, more generally, by computer simulations assuming a steady state of constant population size and selective pressures or neutrality. It is found that the likelihood is, in general, not very dependent on the degree of selection at the loci and is very flat. This suggests that precise information on map position will not be obtained from estimates of linkage disequilibrium.     

How many alleles per locus should be used to estimate genetic distances?

As more microsatellite loci become available for use in genetic surveys of population structure, population geneticists are able to select loci to use in population structure surveys. This study used computer simulations to investigate how the number of alleles at loci affects the precision of estimates of four common genetic distances. This showed that equivalent results could be achieved by examining either a few loci with many alleles or many loci with a few alleles. More specifically, the total number of independent alleles appears to be a good indicator of how precise estimates of genetic distance will be.     

AFLP标记的特点及其在昆虫学研究中的应用

扩增片段长度多态性（AFLP）是一种新兴的很有效的分子遗传标记方法, 它通过对基因组DNA限制性内切酶酶切片段进行选择性扩增而揭示多态性,具有快速、经济简便、不需要预先知道模板DNA的信息、模板需要量少、重复性高、结果可靠及具有很高的信息含量等优点。AFLP也具有缺点,主要是标记是显性的,同其他显性标记一样,不能区分杂合体和纯合体,因而不能更好地估算种群遗传的变异,对种群遗传结构的分析不能提供更多的统计信息;AFLP技术较复杂,而且经常使用放射性同位素,对模板DNA质量要求也较高。为了克服AFLP的这些缺点,人们又在其基础上发展了其他相关技术,例如AFRP、SAMPL、DALP和TE-AFLP等。目前AFLP在昆虫方面的应用还不是很多,处于初级阶段,主要应用在生态型鉴定、种群遗传分析、连锁图谱构建等方面,相信随着其技术的发展完善,必将会越来越多地应用于昆虫学的研究中。     

Kin selection and parasite evolution: higher and lower virulence with hard and soft selection

Conventional models predict that low genetic relatedness among parasites that coinfect the same host leads to the evolution of high parasite virulence. Such models assume adaptive responses to hard selection only. We show that if soft selection is allowed to operate, low relatedness leads instead to the evolution of low virulence. With both hard and soft selection, low relatedness increases the conflict among coinfecting parasites. Although parasites can only respond to hard selection by evolving higher virulence and overexploiting their host, they can respond to soft selection by evolving other adaptations, such as interference, that prevent overexploitation. Because interference can entail a cost, the host may actually be underexploited, and virulence will decrease as a result of soft selection. Our analysis also shows that responses to soft selection can have a much stronger effect than responses to hard selection. After hard selection has raised virulence to a level that is an evolutionarily stable strategy, the population, as expected, cannot be invaded by more virulent phenotypes that respond only to hard selection. The population remains susceptible to invasion by a less virulent phenotype that responds to soft selection, however. Thus, hard and soft selection are not just alternatives. Rather, soft selection is expected to prevail and often thwart the evolution of virulence in parasites. We review evidence from several parasite systems and find support for soft selection. Most of the examples involve interference mechanisms that indirectly prevent the evolution of higher virulence. We recognize that hard selection for virulence is more difficult to document, but we take our results to suggest that a kin selection model with soft selection may have general applicability.