Identifying QTLs and Epistasis in Structured Plant Populations Using Adaptive Mixed LASSO

Association analysis in important crop species has generated heightened interest for its potential in dissecting complex traits by utilizing diverse mapping populations. However, the mixed linear model approach is currently limited to single marker analysis, which is not suitable for studying multiple QTL effects, epistasis and gene by environment interactions. In this paper, we propose the adaptive mixed LASSO method that can incorporate a large number of predictors (genetic markers, epistatic effects, environmental covariates, and gene by environment interactions) while simultaneously accounting for the population structure. We show that the adaptive mixed LASSO estimator possesses the oracle property of adaptive LASSO. Algorithms are developed to iteratively estimate the regression coefficients and variance components. Our results demonstrate that the adaptive mixed LASSO method is very promising in modeling multiple genetic effects when a large number of markers are available and the population structure cannot be ignored. It is expected to be a powerful tool for studying the architecture of complex traits in important plant species. Supplemental materials for this article are available from the journal website.     

水稻赖氨酸和总黄酮含量的QTL定位及环境互作分析

为挖掘多环境下稳定存在的水稻赖氨酸和总黄酮含量相关QTL,以粳稻东农425和长白10号及其衍生的180个株系的F_(6:7)重组自交系(RIL)作为供试群体,采用完备区间作图法(ICIM)和基于混合线性模型的复合区间作图法(MCIM),对2014年和2015年水稻的赖氨酸含量和总黄酮含量进行加性QTL定位及环境互作分析。结果检测到10个影响赖氨酸含量的加性效应QTL和12个影响黄酮含量的加性效应QTL,分布在除第9、第10和第12染色体以外的9条染色体上,其中在第5染色体的RM538~RM1271标记区间内连续2年检测到总黄酮含量QTL。检测到6个存在环境互作效应的赖氨酸含量QTL、4个存在环境互作效应的总黄酮含量QTL,互作贡献率为0.15%~6.73%;一对影响总黄酮含量的上位互作效应的QTL,贡献率为0.99%。本研究结果为水稻赖氨酸和总黄酮含量QTL分子标记辅助育种提供了一定的理论依据。     

QTL analysis reveals the genetic architecture of domestication traits in Crisphead lettuce

The genetic architecture of crop domestication is generally characterized by three trends: relatively few genomic regions with major QTL effects are involved, QTL are often clustered, and alleles derived from the crop do not always contribute to the crop phenotype. We have investigated the genetic architecture of lettuce using a recombinant inbred line population from a cross between a crop Lactuca sativa (‘Salinas’) and its wild relative L. serriola. Few genomic regions with major QTL, plus various intermediate QTL, largely control the transition from wild to cultivated Crisphead lettuce. Allelic effects of all major QTL were in the expected direction, but there were intermediate QTL where the crop contributed to the wild phenotype and vice versa. We found two main regions with clusters of QTL, one on linkage group 3, where the crop allele induced lower seed output, another on linkage group 7, where the crop allele caused a delay in flowering time. Potentially, knowledge of genetic changes due to the domestication could be relevant for the chance that a transgene inserted in a crop genome will spread to wild relatives due to hitchhiking effects. If a transgene would be inserted in one of these regions, background selection on the crop alleles may lead to a reduced fitness of hybrids with the transgene. QTL research on the effects of domestication genes can thus indicate regions in the crop genome that are less likely to introgress, although these still need to be verified under field conditions.     

鲍分子遗传学研究进展

阐述了近年来鲍分子遗传学方面的研究进展,总结了核型分析、等位酶、微卫星和小卫星、随机扩增多态性DNA、限制性片断长度多态性、线粒体DNA、表达序列标签研究和基因序列等技术在鲍种群遗传多样性、遗传分化、遗传结构及种质鉴定等方面的应用。并指出今后应加强鲍蛋白质组学、功能基因组学、遗传连锁图谱、数量性状基因座和标记辅助选择等方面研究。     

工程车辆车桥位移谱统计分布建模及分步参数识别

针对非公路用车的车桥实测位移谱统计分布建模中模型选择、参数识别的初值选取主观性大和计算效率低等难题,该文以实测的车桥位移信号为研究对象,分别进行时域分析、频域功率谱分析,对信号进行分组,统计频数,获得统计直方图和累计概率分布曲线。分别采用正态分布、双峰正态分布、威布尔分布和双峰威布尔分布模型对位移谱进行建模,提出分步参数识别方法。引入灰色关联度目标函数,以人工鱼群算法获得的参数作为模型参数的初始值,采用迭代非线性最小二乘法levenberg-marquardt (LM)算法进行精确参数识别,使用相关系数和kolmogorov-smirnov(KS)检验对各模型的拟合优度进行比较。结果表明,混合威布尔分布与统计直方图的相关系数为(0.9800,0.9908,0.9867,0.9665),混合正态分布为(0.9793,0.9904,0.9783,0.9661),威布尔模型为(0.8613,0.9113,0.8618,0.8854),正态模型为(0.8611,0.9127,0.8624,0.8869),混合威布尔模型可以对车桥位移谱进行高精度拟合,而所提出的分步参数识别法可以高效、准确地进行模型的参数识别。研究结果可为车辆疲劳载荷谱的编制和台架试验提供参考。     

采用多源信息融合的妊娠猪舍环境质量评价方法

妊娠猪舍作为养殖场猪只繁育的基础条件,其环境质量对母猪的生产性能有显著影响。为合理评价妊娠猪舍环境质量,该研究提出一种基于模拟退火的粒子群算法（Simulated Annealing-Particle Swarm Optimization,SA-PSO）、套索算法（Least Absolute Shrinkage and Selection Operator,LASSO）和反向传播（Back Propagation,BP）神经网络的环境质量评价模型。利用卡尔曼滤波和分批估计自适应加权融合算法,实现多节点环境数据的时间与空间数据融合;构建猪舍环境质量非线性评价模型,采用LASSO算法,筛选得出与环境质量强相关的特征参数,实现输入降维;融合SA-PSO算法实现网络初始权值和阈值的优化,形成SA-PSO-LASSO-BP神经网络评价模型。通过对数据采集系统获取的实际妊娠猪舍环境数据进行验证,结果表明：提出的环境质量模型决定系数为0.918、总准确率为95.85%,相比单纯使用BP神经网络,加入LASSO和SA-PSO算法后决定系数与总准确率分别提高了37.43%、11.09%,具有更高的评价精度和性能,可更好地拟合复杂环境参数与环境质量间的非线性关系,为妊娠猪舍环境质量评价提供参考。     

基于三重测交群体解析玉米株高与穗位高杂种优势QTL

为检测玉米株高、穗位高杂种优势QTL,以121株intermated B73×Mo17(IBM)个体为基础群体,按照三重测交交配设计构建了三重测交群体,通过完备区间作图法对株高、穗位高杂种优势的主效QTL及互作位点进行了分析。在第9染色体上的2个紧密连锁的区段分别定位到了一个株高、穗位高杂种优势加性QTL位点,单个QTL的表型贡献率为14.3%和18.6%。该QTL可能同时对株高、穗位高杂种优势起作用。在第1、第3染色体上检测到2个株高杂种优势超显性QTL,可解释表型变异的9.0%~11.4%;在第1、第6、第8染色体上检测到5个穗位高杂种优势超显性QTL,可解释表型变异的6.6%~16.8%。进一步分析发现,2对加加上位性互作区段及2对显显上位性互作区段对穗位高杂种优势存在上位性贡献,加加互作效应及显显互作效应可共同解释表型变异的40.7%和26.8%。由此可知,加性、显性及两位点互作上位性共同对株高、穗位高杂种优势存在贡献。本研究检测到的主效QTL位点有助于株高、穗位高在杂种优势育种中的进一步应用。     

水旱稻根基粗、千粒重主效QTL近等基因系的构建及鉴评

近等基因系的选育是分子遗传图谱构建、数量性状基因定位及分子标记辅助育种的重要基础之一。本文利用分子标记辅助目标性状QTL前景选择及恢复轮回亲本基因组的背景选择，再结合表型选择获得了定位在水稻4号、6号染色体上根基粗、千粒重2个主效QTL的近等基因系。其中有9个系入选旱田根基粗主效QTL brt4.1的近等基因系，根基粗的表型值为1.07～1.16mm，较轮回亲本越富提高6.11％～15.18％，平均遗传背景恢复率达97.22％；千粒重主效QTL的近等基因系有11个系入选，千粒重的表型值为21.25～26.25g，较轮回亲本越富的增幅为7.05％～32.16％，平均遗传背景恢复率为95.97％。另外，本文还就分子标记辅助近等基因系选育中背景选择标记数的确定、基于QTL-NILs的基因克隆等进行了讨论。     

Genome-wide association study to identify chromosomal regions related to panicle architecture in rice (Oryza sativa)

Panicle architecture directly affects the grain yield of rice; meanwhile, crop domestication has increased the complexity of rice panicle size and branching pattern. Genome-wide association study (GWAS) was performed to investigate the genetic basis underlying panicle architecture using 183 rice accessions from around the world and a 7 K SNP array. Phenotyping was conducted at Texas A&M AgriLife Research Center in Beaumont, TX. GWAS was performed using MLM (Q?+?K) model using GAPIT software. At p-value?<?0.001, a total of 49 GWAS QTLs controlling various panicle architecture traits were mapped. Considering the recurring and linked SNPs across the panicle architecture traits, 42 independent QTL regions were identified. Among these, 27 QTL regions co-localized with known genes or previously reported QTLs or significant SNP markers, while 15 were potentially novel QTL regions. The results of our study offer useful information on genetic bases controlling panicle architecture in rice, which could be further validated and utilized for designing markers for use in markers assisted selection (MAS) in rice breeding programs.

     

紧凑型糯玉米种质资源的创制与评价

为创制紧凑型糯玉米种质,本研究以紧凑型普通玉米自交系郑58为供体亲本,以平展型糯玉米自交系通759为轮回亲本,通过标记辅助回交结合叶夹角表型选择的方法,转移玉米叶夹角主效QTL(qLA5)有利等位基因,创制了29份紧凑型BC₂F₂单株。48个标记背景选择及高密度下株型、抗逆性、产量、品质等18个性状综合鉴定,筛选出株型紧凑、产量高、抗逆性强、品质优良的糯玉米新种质4份,使轮回亲本平均基因组含量由78.48%提高到88.67%,可作为紧凑型糯玉米育种的亲本材料。本研究结果为利用普通玉米改良糯玉米种质,选育紧凑型优质鲜食糯玉米新品种提供了理论参考。     

Predicting Additive and Non-additive Genetic Effects from Trials Where Traits Are Affected by Interplot Competition

There are two key types of selection in a plant breeding program, namely selection of hybrids for potential commercial use and the selection of parents for use in future breeding. Oakey et al. (in Theoretical and Applied Genetics 113, 809–819, 2006) showed how both of these aims could be achieved using pedigree information in a mixed model analysis in order to partition genetic effects into additive and non-additive effects. Their approach was developed for field trial data subject to spatial variation. In this paper we extend the approach for data from trials subject to interplot competition. We show how the approach may be used to obtain predictions of pure stand additive and non-additive effects. We develop the methodology in the context of a single field trial using an example from an Australian sorghum breeding program.     

优化支持向量机在鲜切生菜加工HACCP分类中的应用

该文介绍了一种基于支持向量机模型解决鲜切生菜加工HACCP（hazard analysis and critical control point）关键控制点智能发现的方法。在通用支持向量机模型进行鲜切生菜加工关键控制点的发现试验中,依靠人工经验选取支持向量机（support vector machine,SVM）核函数参数,识别关键控制点准确率波动较大。该文利用遗传算法优化支持向量机核函数参数的选取,构建了一种基于遗传算法的支持向量机（GA-SVM）模型,应用该模型在鲜切生菜生产关键控制点的发现试验中获得了87.5%的识别率,比传统方法稳定性更高。该方法对其他HACCP关键控制点的智能发现具有很好的借鉴意义。     

玉米叶夹角和叶向值的QTL定位

叶夹角和叶向值是评价玉米株型的重要指标。本研究以甜玉米自交系组合T14×T4的F2为作图群体,构建了包含192个SSR标记位点的遗传连锁图谱,覆盖玉米基因组1260cM,平均图距6.56cM。通过测定F2、F2:3家系的叶夹角和叶向值,应用复合区间作图法在两个世代中共检测到26个QTL,其中14个与叶夹角相关的QTL,分别位于第2、5、6、7和8染色体上,单个QTL可解释的表型变异为3.3%～26.2%;12个与叶向值相关的QTL,分布于第1、2、3、7和10染色体上,单个QTL可解释的表型变异为3.1%～20.7%。在第2、3、5染色体上分别检测到1、1、2个同时在F2、F2:3家系都稳定表达的QTL,分别落在区间bnlg1329～bnlg1613、umc1148～umc2275和umc1097～umc1692,可作为相关数量性状基因的候选基因。发现1个同时控制叶夹角和叶向值性状的QTL,位于第2染色体上的bnlg1017-umc2129区间,对两性状的表型贡献率分别为10.8%和10.6%。本研究的结果有望为玉米耐密型育种及分子辅助选择育种提供一定的理论依据。     

MAPPING OF IRON AND ZINC QUANTITATIVE TRAIT LOCI IN SOYBEAN FOR ASSOCIATION TO IRON DEFICIENCY CHLOROSIS RESISTANCE

Iron deficiency chlorosis (IDC) in soybean results in yield losses or in extreme cases death. Breeding for resistance has shown limited success with no cultivar having complete resistance. Mineral content of the soybean could be an indicator of the ability of the plant to withstand the effects of IDC. Iron (Fe) and zinc (Zn) concentration was examined in soybean seed and leaves. SSR, RFLP, and BARCSOYSSR markers were used to construct a linkage map used for mapping of Fe and Zn concentrations. The QTL analysis for the combined data identified one major QTL for seed Fe accumulation on chromosome 20 that explained 21.5% of the variation. This QTL was in the marker interval pa_515-1-Satt239, with marker pa_515-1 previously being used to map an Fe-efficiency QTL. This provides the first evidence of a potential genetic link between Fe-efficiency and Fe accumulation in the soybean seed.     

作物次级群体的研究进展

用于作物数量性状基因座(QTL)定位研究的次级群体有近等基因系、导入系、染色体片段代换系等。次级群体是用于QTL鉴定、精细定位、互作分析、图位克隆、品种改良等的良好材料。相对于初级群体而言,次级群体是在相似的遗传背景下进行QTL分析,消除了大部分遗传背景的干扰和QTL之间的互作,提高了QTL分析的灵敏度和准确性。概述了作物次级群体库的构建及利用的研究进展,讨论了基于次级群体理论发展起来的染色体单片段代换系在作物遗传育种中的利用价值。     

Landscape changes caused by high altitude ski-pistes affect bird species richness and distribution in the Alps

There is a paucity of research on the wider landscape-level effects of ski-piste construction on alpine fauna. In this study, the response of alpine bird communities to the landscape changes induced by the construction of ski-pistes was investigated in the western Italian Alps. The aims were: (i) to test the hypothesis that ski-pistes have a detrimental effect on alpine grassland bird communities at a landscape-scale; and, (ii) to model local probability distributions of bird species according to different scenarios of ski-piste restoration and ski-piste proliferation above the treeline. Species richness and presence/absence data from point counts were analyzed in relation to GIS-derived landscape variables based on a 16 ha hexagon grid. Predictive variables were selected through the LASSO model selection procedure, and logistic regression was used to estimate the probability of occurrence of each species in each hexagon. Grassland species richness, and probability of occurrence of water pipit, wheatear and black redstart, significantly decreased with increasing extent of ski-piste edge. Length of ski-piste edge was in the set of best models considering a large range of habitat and landscape predictors, and are therefore clearly features that exert a strong negative effect on high alpine grassland bird communities. Predictions of species occurrence were made by applying the models to different scenarios of habitat change. These showed predicted detrimental impacts of a relatively small 10% increase in ski-piste extent, but also that grassland restoration on existing ski-pistes could result in significantly increased occurrence rates of alpine grassland species. This study suggests that ski-pistes are perceived by birds as detrimental features of the alpine landscape. To minimize their impact, new, environmentally–friendly ways of constructing pistes should be developed, which could include habitat restoration and management to obtain a level of grass cover such that edges of ski-pistes are no longer perceived by birds.     

不结球白菜抽薹开花性状的主基因+多基因遗传分析

为了研究不结球白菜抽薹开花性状的遗传规律,并对其耐抽薹品种进行鉴定筛选,以不结球白菜易抽薹纯系M10-1和耐抽薹纯系M10-2杂交获得的6世代(P1、P2、F1、B1、B2和F2)群体为材料,利用植物数量性状主基因+多基因多世代联合分析的方法对不结球白菜抽薹性状(现蕾期)和开花性状(开花期)进行遗传分析。结果表明,控制抽薹性状的为2对加性-显性-上位性主基因+加性-显性多基因,并存在明显的加性、显性和上位性效应。其中,2对主基因的加性效应值均为正,显性效应值hb大于ha,且以第2对主基因的正向显性效应为主;抽薹性状存在较大的主基因加性×加性和显性×显性互作效应,以呈负向的多基因的加性效应为主。B1、B2和F2的主基因遗传率分别为83.83%、87.82%和88.31%,多基因遗传率均为0,主基因+多基因遗传率平均为86.65%,环境变异占表型变异平均为13.35%,说明抽薹性状主要受主基因控制,在育种上可以应用抽薹性状(现蕾期)作为不结球白菜耐抽薹性的鉴定标准,并可在早期世代对其耐抽薹性进行选择,且要注意一定的环境因素。开花性状与抽薹性状遗传相似,均受到2对主基因控制,但主基因+多基因遗传率平均为9.57%,而环境变异平均为90.43%,对开花的影响显著,说明开花性状与环境的互作效应非常明显,不适宜作为耐抽薹性的鉴定指标。利用本研究获得的抽薹性状作为不结球白菜耐抽薹性的鉴定指标,并应用于育种实践,对选育不结球白菜耐抽薹新品种,提高产量具有重要意义。     

小麦籽粒淀粉主要特性的QTL定位

为给分子标记辅助选择和小麦品质育种提供依据,以小麦杂交组合99G44×京771重组自交系群体(RIL)为材料,利用SSR分子标记技术,采用复合区间作图法对小麦籽粒淀粉主要特性进行了QTL分析。结果表明,检测出1个与总淀粉含量有关的显著加性效应QTSA.-6B,位于6B染色体,位点总贡献率为10.91%;检测出1个与支链淀粉含量有关的显著加性效应QAmp.-1B,位于1B染色体,位点的总贡献率为9.54%;检测出1个与直链淀粉含量有关的显著加性效应QAms.-6B,位于6B染色体,位点总贡献率为7.29%;检测出1个与支/直比有关的显著加性效应QAmp./Ams.-6B,位于6B染色体,位点的总贡献率为12.69%;检测出1个与高峰粘度有关的显著加性效应QPV-1B,位于1B染色体,位点的总贡献率为5.91%;检测出2个与崩解值有关的显著加性效应QBD-1B和QBD-2D,位于1B、2D染色体,位点总贡献率为12.95%;检测出1个与回生值有关的显著加性效应QSB-1B,位于1B染色体,位点总贡献率为6.99%;检测出1个与低谷粘度有关的显著加性效应QTV-3B,位于3B染色体,位点的总贡献率为5.16%;检测出1个与膨胀势有关的显著加性效应QSP-1B,位于1B染色体,位点总贡献率为7.02%。本研究定位的淀粉品质性状的标记可作为小麦品质分子育种的工具。     

Quantitative Trait Loci for Brown Rice Color,Phenolics, Flavonoid Contents,and Antioxidant Capacity in Rice Grain

Phytochemicals such as phenolics and flavonoids, which are present in rice grains, are associated with reduced risk of developing chronic diseases such as cardiovascular disease, type 2 diabetes, and certain cancers. The phenolic and flavonoid compounds in rice grains also contribute to the antioxidant activity. Biofortification of rice grain by conventional breeding is one way to improve nutritional quality to combat nutritional deficiency. For improvement of the phenolics, flavonoids, and antioxidant capacity, we must understand the genetic bases of the related traits. In the present study, mapping of quantitative trait locus (QTL) for five color parameters, phenolics, flavonoids, and antioxidant capacity was completed using a composite interval mapping approach using a doubled haploid (DH) population. Correlation analysis showed that the five color parameters lightness (L*), redness (a*), yellowness (b*), chroma (C), and hue angle (H°) were intercorrelated. The phenolic content was positively correlated with the flavonoid content and antioxidant capacity (P < 0.001), whereas the flavonoid content had no relationship with antioxidant capacity, but it was positively correlated with color parameters L* and H° (P < 0.05). A total of 21 putative QTL were detected for the eight traits with at least one QTL and as many as four QTL for different traits. Three QTL at the same interval of GA285 and CT580 on chromosome 2 were significant for color parameters L*, b*, and C; the latter two traits also shared another QTL region on chromosome 8. Two QTL on chromosome 2, qPH‐2 and qFL‐2‐1, flanked by CT87 and G1234, were identified for phenolic and flavonoid content with large additive effects, explaining 16.91 and 12.71%, respectively, of the total phenotypic variation. Three QTL located at the same interval of G379A and CT360 on chromosome 7 were detected for color parameters a* and H°, and antioxidant capacity, which might be allelic to the Rd gene that is responsible for the production of the pigment in brown rice. The results of the present study may provide new opportunities for rice breeders with potential markers to improve nutritional quality by marker‐assisted selection approach.     

Molecular and phenotypic diversity of ICARDA spring barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) collection

Plant breeders are interested in using diverse genotypes in hybridization that can segregate for traits of importance with possibility of selection and genetic gain. Information on molecular and agro-morphological diversity helps the breeders reduce the effort for parental selection and helps the advancement of generations. A phenotypic and molecular diversity study, using 24 traits (agronomic and disease) and 6519 SNPs in a diverse collection of 336 spring barley genotypes, was carried out at Marchouch and Jemma Shiam research stations in Morocco. Based on structure and multivariate analyses, strong differentiation between the two- and six-row types were observed. The linkage disequilibrium (LD) decay of the current collection (for the combined population) was up to 3.58 cM (r ² = 0.15) while LD decay were estimated 3.91 and 2.36 cM for two- and six-row barley, respectively. PCA of agro-morphological traits revealed grain per spike, net form of net blotch (NFNB), spot form of net blotch (SFNB), and 1000 kernel weight were the most discriminatory traits in the current collection. Association mapping in the two independent populations will be ideal for identification of markers, and QTL related to traits. The generated information on relatedness between individuals will help identify diverse genotypes for breeding programs.